Genetic information is stored in DNA by means of a triplet code that is nearly universal to all living things on Earth. The genetic code is initially transferred from DNA to RNA, in the process of transcription.

1. Genetic code
and
Transcription
Preparing by : Anfal ALKATEEB

2. General information
Genetic information is stored in DNA by means of a triplet code that is
nearly universal to all living things on Earth.
The genetic code is initially transferred from DNA to RNA, in the process of
transcription.
Once transferred to RNA, the genetic code exists as triplet codons, which
are sets of three nucleotides in which each nucleotide is one of the four
kinds of ribonucleotides composing RNA.
RNA’s four ribonucleotides, analogous to an alphabet of four “letters,” can
be arranged into 64 different three-letter sequences. Most of the triplets in
RNA encode one of the 20 amino acids present in proteins, which are the
end products of most genes.
Several codons act as signals that initiate or terminate protein synthesis.
In eukaryotes, the process of transcription is similar to, but more complex
than, that in prokaryotes and in the bacteriophages that infect them

3. Gene code
In the first step, information present on one of
the two strands of DNA (the template strand) is
transferred into an RNA complement through
the process of transcription.
Once synthesized, this RNA acts as a
“messenger” molecule, transporting the
coded information out of the nucleus hence its
name, messenger RNA (mRNA). The mRNAs
then associate with ribosomes, where
decoding into proteins occurs.

4. Genetic code
• there are two major questions.
1. How is genetic information encoded?
2. How does the transfer from DNA to RNA
occur,
Hhus explaining the process of
transcription?

5. The Genetic Code uses ribo nucleotide
bases as “letters”
• general features of genetic code :
1. The genetic code is written in linear form, using as “letters” the ribonucleotide bases that
compose mRNA molecules. The ribonucleotide sequence is derivednfrom the
complementary nucleotide bases in DNA.
• 2. Each “word” within the mRNA consists of three ribonucleotide letters, thus referred
to as a triplet code. With several exceptions, each group of three ribonucleotides, called a
codon, specifies one amino acid.
• 3. The code is unambiguous—each triplet specifies only a single amino acid.
• 4. The code is degenerate, meaning that a given amino acid can be specified by more than
one triplet codon. This is the case for 18 of the 20 amino acids.
• 5. The code contains one “start” and three “stop” signals, triplets that initiate and terminate
translation, respectively.

6. • 6. No internal punctuation (analogous, for example, to a comma) is used in the
code. Thus, the code is said to be comma less. Once translation of mRNA begins,
• the codons are read one after the other with no breaks between them (until a stop
signal is reached).
• 7. The code is non overlapping. After translation commences, any single
ribonucleotide within the mRNA is part of only one triplet.
• 8. The sequence of codons in a gene is colinear, with the sequence of amino
acids making up the encoded protein.
• 9. The code is nearly universal. With only minor exceptions,
a single coding dictionary is used by almost all viruses,
prokaryotes, archaea, and eukaryotes.

7. Triplet Nature of the
Code
One experimental work of Francis Crick , et al.), provided the first solid
evidence for a triplet code
These researchers induced insertion and deletion mutations in the rII locus
of phage T4 Wild-type phage cause lysis and plaque formation in strains B
and K12 of E. coli.
However, rII mutations prevent this infection process in strain K12, while
allowing infection in strain B. Crick and his colleagues used the acridine dye
proflavin to induce the mutations.
This mutagenic agent intercalates within the double helix of DNA,
causing the insertion or deletion of one or more nucleotides during
replication.

8. The Triplet Nature of the Code
An insertion of a single nucleotide
causes the reading frame to shift,
changing all subsequent
downstream codons.
Such mutations are referred to as
frameshift mutations.
the effect of frameshift mutations on a
DNA sequence repeating the triplet
sequence GAG. (a) the insertion
of a single nucleotide shifts all
subsequent triplets out of the reading
frame.
Upon translation, the amino acid
sequence of the encoded protein
will be altered radically starting at
the point where the mutation
occurred.
A second change might result in a revertant
phage, which would display wild-type behavior
and successfully infect E. coli K12. For
example, if the original mutant contained an
insertion (+), a second event causing a deletion
(−) close to the insertion would restore the
original reading frame.

9. When two pluses or two minuses occurred
in the same sequence, the correct reading
frame was not reestablished.
This argued against a doublet (twoletter)
code.
However, when three pluses or three
minuses were present together, the original
frame was reestablished.
These observations strongly supported the
triplet nature of the code.

10. The Non Overlapping Nature
of the Code
Work by Sydney Brenner and others soon established that the code could not
be overlapping for any one transcript.
If the nucleotide sequence were, say, GTACA, and parts of the central codon,
TAC, were shared by the outer codons, GTA and ACA, then only certain amino
acids those with codons ending in TA or beginning with AC) should be found
adjacent to the one encoded by the central codon.
For example, when any particular central amino acid is considered, only 16
combinations of three amino acids (tripeptide sequences) would theoretically
be possible.
Looking at the amino acid sequences of proteins that were known at that time,
Brenner failed to find such restrictions in tripeptide sequences. For any central
amino acid, he found many more than 16 different tripeptides.
This observation led him to conclude that the code is not overlapping

11. A second major argument against an overlapping code concerned
the effect of a single-nucleotide change. With an overlapping code,
two adjacent amino acids would be affected by such a point
mutation.
However, mutations in the genes coding for the protein coat of
tobacco mosaic virus (TMV), human hemoglobin, and the bacterial
enzyme tryptophan synthetase invariably revealed only single
amino acid changes.
The third argument against an overlapping code was presented by
Francis Crick in 1957, when he predicted that DNA would not serve
as a direct template for the formation of proteins.
Crick reasoned that any affinity between nucleotides and an amino
acid would require hydrogen bonding. Chemically, however, such
specific affinities seemed unlikely.
Crick’s and Brenner’s arguments, taken together, strongly
suggested that, during translation, the genetic code is non
overlapping.
Without exception, this concept has been upheld.

12. The Comma less and Degenerate Nature
of the Code
The basis of genetic evidence, that the code would be comma less that
is, Crick believed no internal punctuation would occur along the
reading frame.
Crick also speculated that only 20 of the 64 possible codons would
specify an amino acid and that the remaining 44 would carry no coding
assignment.
Was Crick wrong with respect to the 44 “blank” codes?
Or is the code degenerate, meaning that more than one codon specifies
the same amino acid?

13. To answer of this question
If such a nonsense codon was encountered during protein synthesis, the
process would probably stop or be terminated at that point.
If so, the product of the rII locus would not be made, and restoration would
not occur.
Because the various mutant combinations were able to reproduce on E.
coli K12, Crick and his colleagues concluded that, in all likelihood, most, if
not all, of the remaining 44 triplets were not blank. It followed that the
genetic code was degenerate. As we shall see, this reasoning proved
to be correct.

14. synthesizing polypeptides in
a Cell-free system
In the cell-free protein-synthesizing system, amino acids are incorporated into
polypeptide chains.
The process begins with an in vitro mixture containing all the essential factors for
protein synthesis in the cell: ribosomes, tRNAs, amino acids, and other molecules
essential to translation.
In 1961, mRNA had yet to be isolated. However, use of the enzyme polynucleotide
phosphorylase allowed the artificial synthesis of RNA templates, which could be
added to the cell-free system.
This enzyme, isolated from bacteria, catalyzes the reaction shown in figure

15. Discovered the enzyme functions metabolically in bacterial cells to degrade
RNA.
However, in vitro, in the presence of high concentrations of ribonucleoside
diphosphates, the reaction can be “forced” in the opposite direction, to
synthesize RNA, as illustrated in the figure.

16. Homopolymer Codes
RNA molecules containing only one type of ribonucleotide, and used them for
synthesizing polypeptides in vitro.
In other words, the mRNA they used in their cell-free protein-synthesizing
system was either UUUUUU . . . , AAAAAA . . . , CCCCCC . . . , or GGGGGG. .
They tested each of these types of mRNA to see which, if any, amino acids were
consequently incorporated into newly synthesized proteins.

17. • Note that the specific triplet codon assignments were
possible only because homopolymers were used.
• In this method, only the general nucleotide composition of
the template is known, not the specific order of the
nucleotides in each triplet, but since three identical letters
can have only one possible sequence (e.g., UUU), three of
the actual codons for phenylalanine, lysine, and proline
could be identified.

18. Mixed Copolymers :
• With the initial success of these techniques, researchers turned to the use
of RNA heteropolymers.
In their next experiments, two or more different ribonucleoside diphosphates
were used in combination to form the artificial message.
Suppose that only A and C are used for synthesizing the mRNA, in a ratio of
1A:5C. The insertion of a ribonucleotide at any position along the RNA molecule
during its synthesis is determined by the ratio of A:C..
Therefore, there is a 1/6 possibility for an A and a 5/6 chance for a C to occupy
each position. On this basis, we can calculate the frequency of any given triplet
appearing in the message.

19. By examining the percentages of the
different amino acids incorporated
into the polypeptide synthesized
under the direction of this message,
we can propose probable base
compositions for each of those
amino acids.
Because proline appears 69 percent
of the time, we could propose that
proline is encoded by CCC (57.9
percent) and also by one of the
codons consisting of 2C:1A (11.6
percent).

20. The Triplet-Binding Assay
In one technique took advantage of the observation that ribosomes, when
presented in vitro with an RNA sequence as short as three ribonucleotides,
will bind to it and form a complex similar to what is found in vivo.
The triplet RNA sequence acts like a codon in mRNA, attracting a tRNA
molecule containing a complementary sequence.
Such a triplet sequence in tRNA, that is, complementary to a codon of mRNA,
is known as an anticodon.

21. This Table 13.2 shows 26 triplet codons assigned
to ten different amino acids.
Eventually, about 50 of the 64
triplets were assigned.
These specific assignments led to
two major conclusions.
First, the genetic code is
degenerate that is, one amino
acid may be specified by more
than one triplet.
Second, the code is also
unambiguous that is, a single
codon specifies only one amino
acid.
The triplet-binding technique was
a major innovation
in the effort to decipher the
genetic code.

22. Repeating Copolymers
a dinucleotide made in this way
is converted to an mRNA with two
repeating triplet codons.
A trinucleotide is converted into
an mRNA that can be read as
containing one of three potential
repeating triplets, depending on
the point at which initiation occurs.
Finally, a tetranucleotide creates
a message with four repeating
triplet sequences.

23. The Coding dictionary reveals Several Interesting
Patterns among the64 Codons
• The various techniques applied to decipher the genetic code have yielded a
dictionary of 61 triplet codons assigned to amino acids.
• The remaining three codons are termination signals, not specifying any amino
acid.
• NOTE : The various techniques applied to decipher the genetic code have
yielded a dictionary of 61 triplet codons assigned to amino acids.
• The remaining three codons are termination signals, not specifying any amino
acid.

24. Degeneracy and the wobble
Hypothesis
all amino acids are specified by two, three,
or four different codons.
3 amino acids (serine, arginine,& leucine)
are each encoded by 6 different codons.
Only tryptophan and methionine are
encoded by single codons.
Most often sets of codons specifying the
same amino acid are grouped, such that
the first two letters are the same, with only
the third differing.
Crick’s hypothesis predicted that the initial
two ribonucleotides of triplet codes are
often more critical than the third member
in attracting the correct tRNA.

25. • He postulated that hydrogen bonding at the third position of the codon–
anticodon interaction would be less spatially constrained and need not
adhere as strictly to the established base-pairing rules.
• Consistent with the wobble hypothesis and the degeneracy of the code, U
at the first position (the 5′ end) of the tRNA anticodon may pair with A or G
at the third position (the 3′ end) of the mRNA codon, and G may likewise
pair with U or C. Inosine (I), one of the modified bases found in tRNA may
pair with C, U, or A. As a result of these wobble rules, only about 30
different tRNA species are necessary to accommodate the 61 codons
specifying an amino acid.

26. The wobble hypothesis proposes a more flexible set of base-pairing rules at
the third position of the codon.
Current estimates are that 30 to 40 tRNA species are present in bacteria
and up to 50 tRNA species in
animal and plant cells.

27. The Ordered Nature of the Code
ordered genetic code.
Chemically similar amino acids often share one or two “middle” bases in the
different triplets encoding them.
For example, either U or C is often present in the second position of triplets that
specify hydrophobic amino acids, including valine and alanine, among others.
Two codons (AAA and AAG) specify the positively charged amino acid lysine.
If only the middle letter of these codons is changed from A to G (AGA and
AGG), the positively charged amino acid arginine is specified.
Hydrophilic amino acids, such as serine or threonine are specified by triplet
codons with G or C in the second position.
The end result of an “ordered” code is that it buffers the potential effect of
mutation on protein function.
While many mutations of the second base of triplet codons result in a change of
one amino acid to another, the change is often to an amino acid with similar
chemical properties.
In such cases, protein function may not be noticeably altered.

28. Initiation, Termination, and suppression
Initiation of protein synthesis in vivo is a highly specific process.
In bacteria, the initial amino acid inserted into all polypeptide chains is a
modified form of methionine—N-formylmethionine (fmet)
Only one codon, AUG, codes for methionine, and it is sometimes called the
initiator codon.
In bacteria, either the formyl group is removed from the initial methionine upon
completion of synthesis of a protein, or the entire formylmethionine residue is
removed.
In eukaryotes, unformylated methionine is the initial amino acid of polypeptide
synthesis.
As in bacteria, this initial methionine residue
may be cleared from the polypeptide.

29. As mentioned in the preceding section, three other codons (UAG, UAA, and
UGA) serve as termination codons, punctuation signals that do not code for
any amino acids . They are not recognized by a tRNA molecule, and translation
terminates when they are encountered.
Mutations that produce any
of the three codons internally
in a gene also result in
termination.
In that case, only a partial
polypeptide is synthesized,
since it is prematurely
released from the ribosome.
When such a change occurs
in the DNA, it is called a
nonsense mutation.

30. The Genetic Code has been
Confirmed in Studies of Phage MS2
• MS2 is a bacteriophage that infects E. coli. Its nucleic acid (RNA) contains only
about 3500 ribonucleotides, making up only three genes.
• These genes specify a coat protein, an RNA-directed replicase, and a
maturation protein (the A protein.)
• The linear sequence of triplet codons formed by the nucleotides corresponds
precisely with the linear sequence of amino acids in the protein.
• Furthermore, the codon for the first amino acid is AUG, the common initiator
codon; the codon for the last amino acid is followed by two consecutive
termination codons, UAA and UAG.
• The analysis clearly of MS2 genes, showed that the genetic code in this virus
was identical to that established in bacterial systems.
• Other evidence suggests that the code is also identical in
eukaryotes, thus providing confirmation of what seemed to
be a universal code.

31. The Genetic Code Is nearly
universal
• The genetic code would be found to be universal, applying equally to viruses,
bacteria, archaea, and eukaryotes.
• Certainly, the nature of mRNA and the translation machinery seemed to be
very similar in these organisms.
• THe coding properties of DNA derived from mitochondria (mtDNA) of yeast
and humans undermined the hypothesis of the universality of the genetic
language. Since then, mtDNA has been examined in many other organisms.
• Cloned mtDNA fragments were sequenced and compare with the amino acid
sequences of various mitochondrial proteins, revealing several exceptions to
the coding dictionary.

32. Most surprising was that the codon
UGA, normally specifying termination,
specifies the insertion of tryptophan
during translation in yeast and human
mitochondria.
In human mitochondria, AUA, which
normally specifies isoleucine, directs
the internal insertion of methionine.
In yeast mitochondria, threonine is
inserted instead of leucine when CUA
is encountered in mRNA.

33. different Initiation Points Create
overlapping Genes
Earlier we stated that the genetic code is nonoverlapping, meaning that each
ribonucleotide in the code for a given polypeptide is part of only one codon.
This concept of overlapping genes is illustrated in (a).
Note that gene is also referred to as an ORF, or open reading frame, which is
defined as a DNA sequence that produces an RNA that has a start and stop
codon, between which is a series of triplet codons specifying the amino acids
making up a polypeptide.
Thus, we sometimes also refer to overlapping ORFs.
Translation initiated at two different
AUG positions out of frame with
one another will give rise
to two distinct amino acid
sequences.

34. • The sequences specifying the K and B polypeptides are initiated in separate
reading frames within the sequence specifying the A polypeptide.
• The K gene sequence overlaps into the adjacent sequence specifying the
C polypeptide.
• The E sequence is out of frame with, but initiated within, that of the D
polypeptide.
• Finally, the A′ sequence, while in frame with the A sequence, is initiated in
the middle of the A sequence.
• They both terminate at the identical point. In all, seven different
polypeptides are created from a DNA sequence that might otherwise have
specified only three (A, C, and D).

35. • A single mutation in the middle of the B gene could potentially affect three
other proteins (the A, A′, and K proteins).
• It may be for this reason that, while present, overlapping genes are not the
rule in other organisms.
• More recently, genomic analysis has made it possible to examine extensive
DNA sequence information in eukaryotes, revealing that the concept of
overlapping genes also applies to these organisms, including mammals.

36. Transcription Synthesizes rnA on
DNA template
• From all studies that it was quite clear that proteins were the end products of
many genes.
• The complex, multistep process begins with the transfer of genetic information
stored in DNA to RNA.
The central question was how DNA, a nucleic
acid, is able to specify a protein composed of
amino acids,?

37. The process by which RNA molecules are
synthesized on a DNA template is called
transcription.
The process by which RNA molecules are
synthesized on a DNA template is called
transcription..
It results in an mRNA molecule
complementary to the gene sequence of one
of the two strands of the double helix.
Each triplet codon in the mRNA is, in turn,
complementary to the anticodon region of its
corresponding tRNA, which inserts the correct
amino acid into the polypeptide chain during
translation.
The significance of transcription is enormous,
for it is the initial step in the process of
information flow within the cell.

38. 1. DNA is, for the most part, associated with
chromosomes in the nucleus of the
eukaryotic cell.
• However, protein synthesis occurs in
association with ribosomes located outside
the nucleus, in the cytoplasm. Therefore
DNA does not appear to participate directly
in protein synthesis.
• 2. RNA is synthesized in the nucleus of
eukaryotic cells, in which DNA is found, and
is chemically similar to DNA.
• 3. Following its synthesis, most RNA
migrates to the cytoplasm, in which protein
synthesis (translation) occurs.
• 4. The amount of RNA is generally
proportional to the amount of protein in a
cell.

39. Initiation, Elongation, and
Termination of RNA synthesis
• 1. Once RNA polymerase has recognized and bound to the promoter, DNA is
converted from its double-stranded form to an open structure, exposing the
template strand.
• 2. The enzyme then proceeds to initiate
RNA synthesis, whereby the first 5′-ribonucleoside
triphosphate, which is complementary to the
first nucleotide, is inserted at the start site.

40. • Subsequent ribonucleotide complements are inserted and linked together
by phosphodiester bonds as RNA polymerization proceeds.
• This process continues in a 5′ to 3′ direction (in terms of the nascent RNA),
creating a temporary 8-bp DNA/RNA duplex whose chains run antiparallel
to one another

41. In E. coli, this process proceeds
at the rate of about 50
nucleotides/second at 37°C.
Like DNA polymerase, RNA
polymerase can perform
proofreading as it adds each
nucleotide.
It is capable of recognizing
a mismatch where a non
complementary base has
been inserted.
In such a case, the enzyme
backs up and removes the
mismatch.
It then reverses direction and
continues elongation

42. • The enzyme traverses the entire gene until eventually it encounters a
specific nucleotide sequence that acts as a termination signal.
• Such termination sequences, about 40 base pairs in length, are extremely
important in prokaryotes because of the close proximity of the end of one
gene to the upstream sequences of the adjacent gene.
• The unique sequence of nucleotides in this termination region causes the
newly formed transcript to fold back on itself, forming what is called a
hairpin secondary structure, held together by hydrogen bonds
• The hairpin is important to termination. In some cases, the termination of
synthesis is also dependent on the
termination factor, rho (R).

43. • Wherever an A, T, C, or G residue was encountered there, a corresponding
U, A, G, or C residue, respectively, was incorporated into the RNA
molecule. These RNA molecules ultimately provide the information leading
to the synthesis of all proteins in the cell.
The result is that during transcription, a large
mRNA is produced, encoding more than one
protein. Since genes in bacteriophages are
sometimes referred to as complementation
groups and are called cistrons the RNA is called a
polycistronic mRNA.
The products of genes transcribed in this fashion
are usually all needed by the cell at the same
time, so this is an efficient way to transcribe and
subsequently translate the needed genetic
information.
In eukaryotes, monocistronic mRNAs are the
rule, although an increasing number of exceptions
are being reported.

44. Transcription in eukaryotes differs from
Prokaryotic transcription in Several ways
1. Transcription in eukaryotes occurs within the nucleus under the direction of
three separate forms of RNA polymerase.
Unlike the prokaryotic process, in eukaryotes the RNA transcript is not free to
associate with ribosomes prior to the completion of transcription.
For the mRNA to be translated, it must move out of the nucleus into the
cytoplasm.

45. 2. Initiation of transcription of eukaryotic genes requires the compact chromatin
fiber, characterized by nucleosome coiling, to be uncoiled and the DNA to be
made accessible to RNA polymerase and other regulatory proteins.
This transition, referred to as chromatin remodeling, reflects the dynamics involved
in the conformational change that occurs as the DNA helix is opened
3. Initiation and regulation of transcription entail a more extensive interaction
between cis-acting DNA sequences and trans-acting protein factors involved in
stimulating and initiating transcription.
Eukaryotic RNA polymerases for example, rely on transcription factors (TFs) to
scan and bind to DNA.
In addition to promoters, other control units, called enhancers and silencers, may
be located in the 5′ regulatory region upstream from the initiation point, but they
have also been found within the gene or even in the 3′ downstream region,
beyond the coding sequence.

46. • An initial processing step involves the addition of a 5′ cap and a 3′ tail to
most transcripts destined to become mRNAs.
• The initial (or primary) transcripts are most often much larger than those
that are eventually translated into protein. Sometimes called pre-mRNAs,
these primary transcripts are found only in the nucleus and referred to
collectively as heterogeneous nuclear RNA (hnRNA). Only about 25 percent
of hnRNA molecules are converted to mRNA.

47. Initiation of Transcription in
Eukaryotes
Eukaryotic RNA polymerase exists in three distinct forms.
While the three forms of the enzyme share certain polypeptide subunits, each
nevertheless transcribes different types of genes,
Each enzyme is larger and more complex than the single prokaryotic
polymerase. For example, in yeast, the holoenzyme consists of two large
subunits and 10 smaller subunits

48. • In regard to the initial template-binding step and promoter regions, most is
known about RNA polymerase II (RNAP II), which is responsible for the
transcription of a wide range of genes in eukaryotes
• The activity of RNAP II is dependent on both:::::
• cis-acting elements surrounding the gene itself
• and a number of trans-acting transcription factors that bind to these DNA
elements

49. • At least four cis-acting DNA elements regulate the initiation of transcription
by RNAP II. :
• The first of these elements, the core promoter, determines where RNAP II
binds to the DNA and where it begins copying the DNA into RNA.
• The other three types of regulatory DNA sequences, called proximal-
promoter elements, enhancers, and silencers, influence the efficiency or the
rate of transcription initiation by RNAP II from the core-promoter element.
Recall that in prokaryotes, the DNA sequence recognized by RNA
polymerase is also called the promoter

50. • In eukaryotes, however, transcriptional initiation is controlled by regulatory
proteins that bind to a larger number of cis-acting DNA elements
• Although eukaryotic promoter elements can determine the site and general
efficiency of initiation, other elements, known as enhancers and silencers,
have more dramatic effects on eukaryotic gene transcription

51. recent Discoveries Concerning
RNA polymerase function
• The enzyme is confronted with its substrate DNA that, unlike in bacteria, is
wrapped around histone proteins organized into nucleosomes.
• RNAP II in yeast contains two large subunits and ten smaller ones, forming a
huge three-dimensional complex with a molecular weight of about 500 kDa.
Promoter DNA initially positions itself over a cleft formed between the two
large subunits of RNAP II.
• Complementary RNA synthesis is then initiated on the DNA template strand
• In summery , an unstable complex is formed during the initiation of
transcription, stability is established n once elongation manages to create a
duplex of sufficient size, elongation proceeds, and then instability again
characterizes termination of transcription

52. Processing Eukaryotic RNA:
Caps and Tails
While in bacteria the base sequence of DNA is transcribed into an mRNA
that is immediately and directly translated into the amino acid sequence as
dictated by the genetic code.
eukaryotic RNA transcripts require significant alteration before they are
transported to the cytoplasm and translated.
All experimental showed that eukaryotic mRNA is transcribed initially as a
precursor molecule much larger than that which is translated into protein.
This initial transcript of a gene must be processed in the nucleus before it
appears in the cytoplasm as a mature mRNA molecule.

53. Modification to Eukaryote pre- mRNA.
A 7- methylguanosine cap is added to the 5- end of the primary transcript by
a 5- __5- phosphate linkage. ( stability and protection)
A poly A tail ( 20-200) nucleotide poly adenosine tract, (As) is added to 3-
end of the transcript.
The 3- end is generated by cleavage rather than by termination ( stability
and protection)

54. The cap stabilizes the mRNA by protecting the 5′ end of the molecule from
nuclease attack.
It is thought to simplify the transport of mature mRNAs across the nuclear
membrane into the cytoplasm and in the initiation of translation of the
mRNA into protein.
That both pre-RNAs and mRNAs contain at their 3′ end a stretch of as
many as 250 a denylic acid residues.
Poly A has now been found at the 3′ end of almost all mRNAs studied in a
variety of eukaryotic organisms.
In fact, poly-A tails have also been detected in some prokaryotic
mRNAs
What the function of this
addtions

55. • While the AAUAAA sequence is not found
on all eukaryotic transcripts, it appears to be
essential to those that have it. If the
sequence is changed as a result of a
mutation, those transcripts that would
normally have it cannot add the poly-A tail.
In the absence of this tail, these RNA
transcripts are rapidly degraded.
• Both the 5′ cap and the 3′ poly-A tail are
critical if an mRNA transcript is to be
transported to the cytoplasm and translated.

56. the Coding regions of
eukaryotic Genes Are Interrupted by
Intervening Sequences Called Introns
The researchers are presented direct evidence that the genes of animal
viruses contain internal nucleotide sequences that are not expressed in
the amino acid sequence of the proteins they encode.
These internal DNA sequences are represented in initial RNA
transcripts, but they are removed before the mature mRNA is translated.

57. Such nucleotide segments are called intervening sequences. DNA
sequences that are not represented in the final mRNA product are also
called introns (“int” for intervening), and those retained and expressed are
called exons (“ex” for expressed).
Splicing involves the removal of the corresponding ribonucleotide
sequences representing introns as a result of an excision process and the
rejoining of the regions representing exons

58. In eukaryotic genes, there are two approaches have been most fruitful for this
purpose.::
1. involves the molecular hybridization of purified, functionally mature mRNAs
with DNA containing the genes from which the RNA was originally transcribed.
• Hybridization between nucleic acids that are not perfectly complementary results
in heteroduplexes, in which introns present in the DNA but absent in the mRNA
loop out and remain unpaired. Intervening sequences in various eukaryotic
genes. the numbers indicate the number of nucleotides present in various intron
and exon regions
The chicken ovalbumin complex shown in the figure is
a heteroduplex with 7 loops (A through G),
representing seven introns whose sequences are
present in the DNA but not in the final mRNA.

59. 2. : provides more specific information. It involves a direct comparison of
nucleotide sequences of DNA with those of mRNA and their correlation with
amino acid sequences.Such an approach allows the precise identification of
all intervening sequences.
Thus far, most eukaryotic genes have been shown to contain introns.
Philip & Richard were studied the B-
globin gene in mice and rabbits
1. The mouse gene contains an intron
550 nucleotides long, beginning
immediately after the codon specifying
the 104th amino acid.

60. In the rabbit, there is an intron of 580 base pairs near the codon for
the 110th amino acid.
In addition, another intron of about 120 nucleotides exists earlier in
both genes.
Similar introns have been found in the b-globin gene in all
mammals examined..