1. NUCLEIC ACIDS AND PROTEIN SYNTHESIS CHAPTER 25 25.1 INTRODUCTION
The nucleic acids, deoxyribonucleic (DNA) and ribonucleic
(RNA) , are, respectively , the molecules that preserve here-
ditary information and that transcribe and translate it in a way
that allows the synthesis of all the varied proteins of the cell
NUCLEOTIDES AND NUCLEOSIDES

2. Mild degradations of nucleic acids yield their monomeric units,
compounds that are called nucleotides.
Complete hydrolysis of a nucleotide furnishes:
A heterocyclic base, either a purine or pyrimidine.
a five-carbon monosaccharide, either D-ribose or 2-deoxy-
D-ribose.
3. A phosphate ion.

3. The central portion of the nucleotide is the monosaccharide and it is
always present as a five-membered ring, that is, as a furanoside.
The nucleosides that can be obtained from DNA all contain 2-deoxy-
D-ribose as their sugar component and one of four heterocyclic bases,
either adenine, guanine, cytosine, or thymine.

4. The nucleosides obtained from RNA contain D-ribose as their sugar
component and either adenine, guanine, cytosine, or uracil as their
heterocyclic base.
Nucleotides are named in several ways. Adenylic acid, for example,
is sometimes called 5’-adenylic acid, it is also called 5’-phosphate,
or simply adenosine monophosphate(AMP).

5. The names and structures of the nucleoside found in DNA and RNA:

7. 25.3 LABORATORY SYNTHESIS OF NUCLEOSIDES
AND NUCLEOTIDES
One technique uses reaction that assemble the nucleoside from
suitably activated and protected ribose derivatives and heterocyclic
base.
Another technique involves formation of the heterocyclic base on
a protected ribosylamine derivative.

8. The third technique involves the synthesis of a nucleosides with a
substituent in the heterocyclic ring that can be replaced with other
groups.

9. Specific phosphorylation of the 5’-OH can be achieved if the 2’- and
3’-OH groups of the nucleoside are protected by an isopropylidene
group.
25.3A MEDICAL APPLCATIONS

10. The discovering of the 6-mercaptopurine led to the development of
other purine derivatives and related compounds. For example:
DEOXYRIBONUCLEIC ACID: DNA
25.4A PRIMARY STRUCTURE
Nucleotides bear the same relation to a nucleic acid that amino
acids do to a protein; they are its monomeric units.

11. Phosphate ester linka
the 3’-OH of one ribose
with the 5’-OH of anther
The connection liks
in protein are amino
groups; in nucleic acids
they are phosphate ester
linkages.

12. 25.4B SECONDARY STRUCTURE
The secondary structure of DNA is important because it enables us
to understand how the genetic information is preserved, hoe it can
be passed on during the process of cell division, and how it can be
transcribed to provide a template for protein synthesis.
Chargaff pointed out that for all species examined:
1. The total mole percentage of purines is approximately equal to
that of the pyrimidines, that is, (%G +%A) / (%C + %T) ≈1
2. The mole percentage of adenine is nearly equal to that of thymine
(i.e.. %A / %T≈1) and the mole percentage of guanine is nearly
equal to that of cytosine (i.e.. %G / %C≈1)
3. The ratio that varies from species is the ratio (%A + %T) / (%G
+ %C).

13. Watson and Crick had X-ray that gave them the bond lengths and
angles of the purines and pyrimidines of model compounds. They
also observed that the internal distance of the double helix is such
that it allows only a purine-pyrimidine. Type of hydrogen bonding
between base pairs.
Base pairing through hydrogen bonds can in only a specific way:
Specific base pairing of this kind is consistent with Chargaff’s
finding that the %A / %T≈1 and that the %G / %C≈1.

14. The two chains of DNA are complementary. Where adenine appears
in one chain, thymine must appear opposite it in the other; wherever
cytosine appears in one chain, guanine must appears in the other. A
always pairs with T and G always pairs with C.
25.4C REPLICATION OF DNA
Just prior to cell division the double strand of DNA begins at one end.
complementary strands are formed along each chain.
There are approximately 6 billion base pairs in the DNA of a
single human cell.
(b) The weight of DNA in a single human cell is
RNA AND PROTEIN SYNTHESIS

15. Protein synthesis requires that two major process take place; the first
takes place in the cell nucleus, the second in the cytoplasm. The first
is transcription, a process in which the genetic messenger is trans-
cribed on to a form of RNA, called messenger RNA(mRNA). The
second pro-cess involves two other forms of RNA, called ribosomal
RNA(rRNA) and Transfer RNA (tRNA).
25.5A MESSENGER RNA SYNTHESIS—TRANSCRIPTION
Protein synthesis begins in the cell nucleus with the synthesis of
mRNA. The ribonucleotide units of mRNA are joined into a chain
by an enzyme called RNA polymerase then the chain separate into
mRNA.
Then the mRNA migrates into the cytoplasm where it acts as a
template for protein synthesis.

16. 25.5B RIBOSOMES—rRNA
Scattered throughout the cytoplasm of most cells are small
bodies called ribosomes.
Although the ribosomes are at the site of protein synthesis,
rRNA itself does not direct protein synthesis. Instead, a number of
ribosomes become attached to a chain of mRNA and form what is
called a polysome.
One of the function of rRNA is to bind the ribosome to the
mRNA chain.
25.5C TRANSFER RNA
Transfer RNA has a much low molecular weight and much more
soluble than mRNA or rRNA. The function of tRNA is to transport
amino acids to specific areas of the mRNA of the polysome.

17. 25.5D THE GENETIC CODE
Genetic code: triplet on mRNA corresponds to amino acid.
The code must be in the form of three bases, because there are 20
different amino acids used in protein synthesis but there are only
four different bases in mRNA.
Lets see the synthesis of a hypothetical polypeptide:
A tRNA bearing Metformyl uses its anticodon to associate with the
proper codon(AUG) on that portion of mRNA that is in contact
with a ribosome. The next triplet of bases on this particular mRNA
chain is AAA; this is the codon that specifies lysine. A lysyl-tRNA
with the matching anticodon UUU attaches itself to this site. The
two amino are in the proper position for an enzyme to join them
in peptide linkage. Then the ribosome moves down in contract

18. with the next codon. This one, GUA, specifies valine. A tRNA
bearing valine binds itself to this site. Another enzymatic
reactions takes place attaching valine to the polypeptide chain.
Then the whole process repeats itself again and again. Even before
the polypeptide chain is fully grown, it begins to form its own
specific secondary and tertiary structure.
DETERMINING THE BASE SEQUENCE OF DAN
The basic strategy of sequencing DNA includes cleaving them into
manageable fragments, identifying points of overlap, and revealing
the nucleotide sequence of the original nucleic Acid.
The first part of the process is accomplished by using enzymes
called restriction endonucleases. These enzymes cleave double-
stranded DNA at specific base sequences. Sequencing of the frag-
ments can be done chemically or with the aid of enzymes.

19. 25.6A CHEMICAL SEQUENCING
The double-stranded restriction fragment to be sequenced is
enzymatically, separated , isolated and treated the labeled fragment
with reagent. For example, if we had a chain like the following:
Treating the fragment with hydrazine. This will produce the
following set of 5’-labeled fragment.

20. These fragment can then be separated by a technique called gel
electrophoresis.
The DNA to be sequenced may be cleaved next to specific pairs
by subjecting it in separate aliquots to four different treatment.
After cleavage, the separate aliquots are subjected to simultaneous
electrophoresis in four parallel tracks of the gel. After autoradio-
graphy, the results allow reading of the DNA sequence directly
from the gel.
LABORATORY SYNTHESIS OF
OLIGONUCLEOTIDES
The traditional approach to genetics involves randomly altering
or deleting genes by inducing mutations in an organism, and then
observing the effects in its progeny. With high organism, the
method is disadvantage.

21. The new approach-reverse genetics is to start with a cloned gene and
to manipulate it in order to find out how it functions. One of the
manipulation is to synthesize strands of DNA which called antisense
nucleotides, are capable of binding with what is called the sense
sequence of the DNA. In doing so, they can alter the activity of the
gene, or even turn it off entirely. For example, if the sense portion
of DNA in a gene read:
A—G—A—C—C—G—T—G—G
The antisense oligonucleotide would read:
T—C—T—G—G—C—A—C—C
Synthesis of such oligonucleotides is an active area of research
today and is directed at many viral diseases, including AIDS.

22. 25.8 THE POLYMERASE CHAIN REACTION
The polymerase chain reaction (PCR) is an extraordinarily simple
and effective method for amplifying DNA sequences.
The PCR has already had a major effect on molecular biology. It is
being used in medicine to diagnose infectious and genetic diseases.
it is now being applied to the prenatal diagnosis of a number of
genetic diseases, including muscular dystrophy, cystic fibrosis and
so on.
The PCR has been used in forensic sciences, in human genetics, and
in evolutionary biology.