This document introduces bio-organic chemistry with a focus on the synthesis and structure of nucleic acids, including DNA and RNA. It explains the roles of nucleotides, transcription, and translation in protein synthesis, as well as the biosynthesis of cholesterol and alkaloids. Additionally, it poses a series of questions related to the topics covered, aiming to deepen understanding of nucleic acids and their biological significance.

1. Unit I: Bio-Organic
chemistry
Dr. V. Sivamurugan
Assistant professor in Chemistry
Pachaiyappa’s College
Chennai – 600 030
E mail; sivaatnus@gmail.com

2. Objectives
1. Synthesis of Pyrimidines and purines.
2. Structure and role of nucleic acids. DNA and RNA Genetic
code.
3. Biosynthesis of cholesterol, phenanthrene alkaloids and
bile acids.

3. Importance of DNA
§ DNA encodes an organism’s entire hereditary information
and controls the growth and division of cells.
§ In most organisms, the genetic information stored in DNA is
transcribed into RNA (Transcription).
§ This information can then be translated for the synthesis of
all the proteins needed for cellular structure and function

4. Nucleosides and Nucleotides
§ Nucleic acids are chains of five-membered-ring sugars linked
by phosphate groups
§ The anomeric carbon of each sugar is bonded to a nitrogen of
a heterocyclic compound in a β-glycosidic linkage

5. Nucleic acids in RNA and DNA
RNA DNA

6. Base pairs

7. Nucleosides - RNA
Adenosine – one donor and one acceptor
Uridine – one donor and one acceptor
Guanosine – one donor and two acceptor
Cytidine – two donors and one acceptor

8. Nucleosides - DNA
Adenosine – one donor and
one acceptor
Uridine – one donor and one
acceptor
Guanosine – one donor and
two acceptor
Thymidine – two donors and
one acceptor

9. Nucleotide
§ A nucleotide is a nucleoside with either the 5’-or the 3’-OH
group bonded in an ester linkage to phosphoric acid.
§ The nucleotides of RNA—where the sugar is D-ribose—are
more precisely called Ribonucleotides.
§ The nucleotides of DNA—where the sugar is 2-deoxy-D-
ribose—are called Deoxyribonucleotides.

10. The Nucleic Acids
§ Nucleic acids are composed of long strands of
nucleotide subunits linked by phosphodiester bonds.
§ These linkages join the 3’-OH group of one
nucleotide to the 5’-OH group of the next nucleotide.
§ DNA and RNA are polynucleotides
§ In a nucleotide at one end of the strand has an
unlinked 5’-triphosphate group, and the nucleotide at
the other end of the strand has an unlinked 3’-
hydroxyl group.
§ DNA is synthesized by enzymes called DNA
polymerases.
§ RNA is synthesized by enzymes called RNA
polymerases.
§ The primary structure of a nucleic acid is the
sequence of bases in the strand.

11. Formation of
complementry base
pairs
• [adenine] = [thymine]
• [guanine] = [cytosine]
• Adenine (A) always paired with thymine (T)
• Guanine (G) always paired with cytosine (C)
• Base pairing in DNA: Adenine and thymine
form two hydrogen bonds;
• cytosine and guanine form three hydrogen
bonds

12. DNA secondary structure
§ The two DNA strands are antiparallel—they run in opposite
directions, with the sugar–phosphate backbone on the
outside and the bases on the inside
5’ --à 3’

13. DNA tertiary structure
The DNA double helix.

14. Major groove and
minor groove
§ DNA can exist in the three different helical forms
§ The major groove occurs where the backbones
are far apart, the minor groove occurs where
they are close together. The grooves twist around
the molecule on opposite sides. Certain proteins
bind to DNA to alter its structure or to regulate
transcription (copying DNA to RNA) or replication
(copying DNA to DNA).

15. Biosynthesis of DNA: Replication

16. Biosynthesis of RNA: Transcription
§ The sequence of DNA bases provides the blueprint for the synthesis of RNA.
§ The synthesis of RNA from a DNA blueprint, called transcription, takes
place in the nucleus of the cell.
§ This initial RNA is the precursor to all RNA: messenger RNA, ribosomal RNA,
and transfer RNA.
§ The newly synthesized RNA leaves the nucleus, carrying the genetic information
into the cytoplasm (the cell material outside the nucleus), where translation of
this information into proteins takes place.
§ DNA contains sequences of bases known as promoter sites. The promoter sites
mark the beginning of genes.
§ An enzyme recognizes a promoter site and binds to it, initiating RNA synthesis.
§ The DNA at a promoter site unwinds to give two single strands, exposing the
bases.
§ One of the strands is called the sense strand or informational strand. The
complementary strand is called the template strand or antisense strand.

17. Transcription: Using DNA as a blueprint for
RNA

18. Biosynthesis of Proteins: Translation
§ A protein is synthesized from its N-terminal end to its C-terminal end by
reading the bases along the mRNA strand in the 5’ ---à 3’ direction.
§ A sequence of three bases, called a codon, specifies a particular
amino acid that is to be incorporated into a protein.
§ Each amino acid is specified by a three-base sequence known as the
genetic code
§ For example, UCA on mRNA codes for the amino acid serine, whereas
CAG codes for glutamine
§ There are four bases and the codons are triplets, 43 = 64 different
codons are possible.
§ 61 Codons specify amino acids and one codon stop protein
synthesis coden called stop codons.
§ Translation is the process by which the genetic message in DNA that
has been passed to mRNA is decoded and used to build proteins.
§ Each of the approximately 100,000 proteins in the human body is
synthesized from a different mRNA.

19. § Transcription (DNA to RNA) is copying within the same
language of nucleotides.
§ Translation (RNA to protein) is changing to another language
—the language of amino acids.

20. Pathway of protein synthesis

21. RNA genetic code

22. The Polymerase Chain Reaction
§ The polymerase chain reaction (PCR) is an extraordinarily
simple and effective method for exponentially multiplying
(amplifying) the number of copies of a DNA molecule.
§ Beginning with even just a single molecule of DNA, the PCR
can generate 100 billion copies in a single afternoon.

23. Biosynthesis of cholesterol

26. Biosynthesis of phenanthrene alkaloid

27. Synthesis purine and pyrimidine bases

28. Baeyer and Fischer synthesis of uric acid

30. Conversion of thiourea into adenine

31. Formamide into adenine

32. Synthesis of guanine

33. University questions
1. Explain the structure of RNA
2. Draw the steps involved in the Biosynthesis of phenanthrene alkaloids
3. Explain the structure of DNA
4. Draw the steps involved in the Biosynthesis of Cholestrol
5. What are the various products obtained by the hydrolysis of nucleic acid under different conditions?
6. How does DNA store information?
7. Draw the structure of uracil and adenine.
8. Describe the secondary structure of DNA.
9. How does DNA direct protein synthesis in a cell?
10. Explain the term genetic-code
11. Explain the role of nucleic acids in biology
12. What are bile acids?
13. Draw the stereochemical structure of cholesterol.
14. What are nucleosides and nucleotides?
15. How will you synthesis cytosine from malondialdehyde —————–– acetal?
16. What is meant by genetic code?
17. Write the structure of cytosine and uracil.
18. Explain the basic steps in biosynthesis of morphine.
19. What is the biological role of DNA?
20. How are the following conversions performed? ureaàuracil, Thio ureaàAdenine.
21. Explain the steps involved in arriving the primary structure of RNA.
22. What is meant by transcription?
23. How many base-pairs in the gene are needed to code for the enzyme Lysozyme (129 amino acids)
found in egg white?
24. Distinguish between DNA and RNA. Nucleic acids on boiling with baryta gives ——————.
25. The systematic name for cytosine is ——————.
26. Discuss the structure and biological role played by RNA.
27. Write a notes on Genetic code.

34. Suggested books