1. Nucleic Acids, Nucleotides, Nucleosides and Bases

2. Overview:
Heredity is the transfer of characteristics anatomical as well as biochemical, from generation to generation. We all know that a pig gives birth to a pig and a mouse gives birth to a mouse.
The transmission of hereditary information from one generation to another took place in the nucleus of the cell.
Chemical analysis of nuclei showed that they are largely made up of special basic proteins called histones and a type of compound called nucleic acids.

3. Nucleic Acids Two kinds of nucleic acids are found in cells:
Ribonucleic acid (RNA), is not found in the chromosomes, but rather is located elsewhere in the nucleus and even outside the nucleus, in the cytoplasm. And there are six types of RNA, all with specific structures and functions.
Deoxyribonucleic acid (DNA), is present in the chromosomes of the nuclei of eukaryotic cells.
Each has its own role in the transmission of hereditary information.

4. Both DNA and RNA are polymers.
nucleic acids are chains.
The building blocks (monomers) of nucleic acid chains are nucleotides.
A nucleotide consists of :
a nitrogenous base
a sugar
one or more phosphate groups

5. A nucleoside = Nitrogen base + Sugar A nucleotide = Nitrogen base +Sugar +Phosphate A nucleic acid = A chain of nucleotides

6. nitrogenous bases
The nitogen bases found in DNA and RNA are basic because they are heterocyclic aromatic amines.
The nitrogenous base is a derivative of
purine or pyrimidines.
Two of these bases-adenine (A) and guanine (G)-
are purines;
The other three-cytosine (C), thymine (T), and uracil (U)-are pyrimidines.
Note that thymine differs from uracil only in the methyl group in the 5 position.

8. In DNA : the purines are adenine (A) and guanine (G)
and the pyrimidines are cytosine (C) and thymine (T)
In RNA : the purines are adenine (A) and guanine (G)
and the pyrimidines are cytosine (C)and uracil (U)
Note that the atoms in the rings of the bases are numbered 1 to 6 in pyrimidine and 1 to 9 purines, whereas the carbons in the pentose are numbered
1' to 5'

9. Sugars
The sugar component of RNA is D-ribose DNA, is 2-deoxy-D-ribose (hence the name deoxyribonucleic acid). .

11. The addition of a pentose sugar to a base produces a nucleoside.
If the sugar is ribose, a ribonucleoside is produced;
if the sugar is deoxyribose, a deoxyribonucleoside is produced.
The ribonucleosides of A, G, C, and U are named adenosine, guanosine, cytidine, and uridine, respectively.
The deoxyribonucleoside of A, G, C, and T have the added prefix, "deoxy-", for example deoxyadenosine
The bases are linked to the monosaccharide by a β-N-glycosidic bond

14. Phosphate
The third component of nucleic acids is phosphoric acid. When this group forms a phosphate ester bond with a nucleoside, the result is a compound known as a nucleotide.

15. Nucleotides are monophosphate, diphosphate, or triphosphate esters of nucleosides.
The first phosphate group is attached by an ester linkage to the 5’-OH of the pentose.
Such a compound is called :
a nucleoside 5'-phosphate or a 5'-nucleotide.
The type of pentose is denoted by the prefix in the names
“ 5' ribonucleotide " and "5'-deoxyribonucleotide

16. a nucleoside monophosphate , like AMP or CMP.
If one phosphate group is attached to the 5'-carbon of the pentose, the structure is:
a nucleoside monophosphate , like AMP or CMP.
If a second or third phosphate is added to the nucleoside, a nucleoside diphosphate (for example, ADP) or triphosphate (for example, ATP) results (Figure 22.4).
The second and third phosphates are each connected to the nucleotide by a "high-energy" bond.
[Note: The phosphate groups are responsible for the negative charges associated with nucleotides, and cause DNA and RNA to be referred to as "nucleic acids."]

19. Most notably, adenosine 5'-triphosphate (ATP) serves as a common currency into which the energy gained from food is converted and stored.

21. What Is the Structure of DNA and RNA?
Nucleic acids, which arc chains of monomers, also have primary, secondary, and higher-order structures.

22. The structure of Nucleic acids Primary Structure of Nucleic acids
Nucleic acids are polymers of nucleotides.
Their primary structure is the sequence of nucleotides.
Note that it can be divided into two parts:
(1) the backbone of the molecule
(2) the bases that are the side-chain groups.

23. The backbone in DNA consists of alternating deoxyribose and phosphate groups.
Each phosphate group is linked to the
3' carbon of one deoxyribose unit and simultaneously to the 5' carbon of the next deoxyribose unit.
Similarly, each monosaccharide unit forms a phosphate ester at the 3' position and another at the 5' position.
As noted earlier, the bases that are linked, one to each sugar unit, are the side chains

25. Figure 8.2: structure of part of DNA chain

26. The primary structure of RNA is the same except that each sugar is ribose (so an -OH group appears in the 2' position) rather than deoxyribose and U is present instead of T.
Thus the backbone of the DNA and RNA chains has two ends: a 3' -OH end and a 5' –phosphate end.

27. Specifically, the 3'-OH of deoxyadenylate is
joined through a phosphoryl group to the
5'-OH of deoxycytidine.

28. Now suppose that deoxyguanylate becomes linked to the deoxycytidine unit of this dinucleotide. The resulting trinucleotide can be represented by an even more abbreviated notation for this trinucleotide is pApCpG or ACG.

30. the base sequence is written in the
The DNA chain has polarity. One end of the chain has 5'-phosphate group and the other end a 3'-OH group
The end of 3'-OH is not linked to another nucleotide.
By convention the symbol ACG means that the
unlinked 5'-phosphate group is on deoxyadenosine
Whereas the unlinked 3'-OH group is on
deoxyguanosine.
the base sequence is written in the
5' → 3' direction.

31. DNA taken from many different species, the quantity of adenine (in moles) is always approximately equal to the quantity of thymine, And the quantity of guanine is always approximately equal to the quantity of cytosine, Although the adenine/guanine ratio varies widely from species to species

32. A. The Watson-Crick DNA double helix
In 1953, James Watson and Francis Crick
deduced the three-dimensional structure of
DNA.
This brilliant accomplishment led the way to an
understanding of gene function in molecular
terms.

33. The important features of their model of DNA are:
1. Two helical polynucleotide chains are coiled
around a common axis. The chains run in
opposite directions.
2. The purine and pyrimidine bases are on the
inside of the helix, whereas the phosphate
and deoxyribose units are on the outside.
The planes of the bases are perpendicular
to the helix axis.
The planes of the bases are perpendicular to the
helix axis.

34. The precise sequence of bases caries the genetic information
3. The two chains are held together by hydrogen
bonds between pairs of bases.
Adenine is always paired with thymine.
Guanine is always paired with cytosine.
4. The sequence of bases along a polynucleotide chain
is not restricted (limited) in any way.
The precise sequence of bases caries the genetic information

35. Figure 8.5 : Two complementary DNA sequences.

36. Figure 8.4 : DNA double helix, illustrating some of its major structural features

37. Watson and Crick model
(a) Schematic representation showing dimensions of the helix. (b) Stick representation showing the backbone and stacking of the bases, (c) space-filling model

38. .
The most important aspect of the DNA double helix is
the specificity of the pairing of bases.
Watson and Crick deduced that:
Adenine must pair with thymine
Guanine with cytosine, because of
Hydrogen-bonding factors.

39. Hence, one member of base pair in a DNA helix must always be a purine and the other a pyrimidine .
The base pairing is restricted by hydrogen-bonding requirements.
Adenine forms two hydrogen bonds with thymine, whereas guanine forms three hydrogen bonds with cytosine.
The orientations and distances of these hydrogen bonds are optimal for achieving strong attraction between the bases.

40. Figure 8.5 : Two complementary DNA sequences.

41. A. In The DNA Double helix
The two chains are coiled around a common axis called the axis of symmetry.
The chains are paired in an antiparallel manner, that is: the 5'-end of one strand is paired with
the 3'-end of the other strand.
The hydrophilic deoxyribose-phosphate backbone of each chain is on the outside of the molecule, whereas the hydrophobic bases are stacked inside.

42. The bases of one strand of DNA are paired with the bases of the second strand
So that an adenine is always paired with a thymine and a cytosine is always paired with a guanine.
Therefore, one polynucleotide chain of the DNA double helix is always the complement of the other.

43. Given the sequence of bases on one chain,
the sequence of bases on the complementary
chain can be determined (Figure 8.6).
The specific base pairing in DNA, leads to
Chargaff’s Rules:
In any sample of double-strand DNA
a) the amount of adenine equals
the amount of thymine
b) the amount guanine equals the amount of cytosine
c) the total amount of purines equals
the total amount of pyrimidines

44. The base pairs are held together by
a) Two hydrogen bonds between A and T
b) Three hydrogen bonds between G and C
These hydrogen bonds, plus the hydrophobic
interactions between the stacked bases
stabilize the structure of the double helix.

45. RNA Structure
RNA molecules are the plates for protein synthesis.
A class of RNA molecules called:
Messenger RNAs (mRNAs)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
Small nuclear RNA (snRNA)
All forms of cellular RNA are synthesized by RNA polymerases that take instructions from DNA templates.
This process of transcription is followed by
Translation: Is the synthesis of proteins according to instructions given by mRNA templates.

46. Several kinds of RNA play roles in gene expression
RNA is a long, unbranched macromolecule consisting of nucleotides joined by 3'  5' phosphodiester bonds
As the name indicates, the sugar unit in RNA is ribose.
The four major bases in RNA are adenine (A), uracil (U), guanine (G), and cytosine (C).

47. Ribonucleotide

48. C T U A G DNA has AGCT RNA has AGCU
The nitrogen base are pyrimidine and purine C T U A G
DNA has AGCT
RNA has AGCU

50. Adenine can pair with uracil, and guanine with cytosine.
The number of nucleotides in RNA range from as few as seventy-five to many thousands.
RNA molecules are usually single stranded, except in some viruses. Consequently :
RNA molecule do NOT have complementary base ratios:
In fact, the proportion of adenine differs from that of uracil
The proportion of guanine differs from that of cytosine, in most RNA molecules.

51. RNA molecules contain regions of double-helical structure that are produced by the formation of hairpin loops (Figure 8.6).
In these regions, A pairs with U, and G pairs with C.
The base pairing in RNA hairpins is frequently
imperfect, G can also form a base pair with U, but it
is less strong than the GC base pair.
Some of the apposing bases may not be complementary at all.

52. Figure 8.6: RNA can fold back on itself to form double-helical region

53. The proportion of helical regions in different kinds of RNA varies over a wide range: a value of 50% is typical.
Messenger RNA (mRNA) molecule:
a) Is produced for each gene or group of
genes that is to be expressed.
b) Is a very heterogeneous class of molecules.

54. Transfer RNA (tRNA):
Carries amino acids in an activated form to the ribosome for peptide-bond formation, in a
sequence determined by the mRNA template.
There is at least one kind of tRNA for each of the twenty amino acids.
It consists of about seventy-five nucleotides, which makes it the smallest of the RNA molecule .

55. Ribosomal RNA (rRNA):
Is the major component of ribosomes.
Ribosomal RNA is the most abundant of the three types of RNA.

56. Small nuclear RNA (snRNA):
A small RNA molecule in the cytosol
Plays a role in the targeting of newly
synthesized proteins.