NUCLEIC ACID METABOLISM COMPLETE NOTES (B.Pharm 2nd Sem) PDF

ORGANIZATION OF MAMMALIAN GENOME
All cells have complete set of DNA called Genome except egg and sperm cell. Genetic
material in prokaryotes and eukaryotes is the DNA. In human a 2 meter long DNA is
packed in a nucleus of about 10um diameter.
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Organization of prokaryotic DNA facebook group and then go to file section
1. In the prokaryotic cell, the DNA is organized as a single chromosome in the form
of double stranded circle.
2. These bacterial chromosomes are packed in the form of nucleoids, by the
interaction with protein and certain cations (Polyamines).
Organization of Eukaryotic DNA

1. In eukaryotes cell nucleus, loose thread DNA with attached proteins is called
chromatin.
2. Chromatin gets organized into compact structure to form chromosome at the time
of cell division.
3. The major proteins involved in chromatin are histone proteins and other non-
histone proteins).
4. One segment (section) of DNA is known as gene (1000s of Gene in one
chromosome)
5. Each core with two turns of DNA wrapped round it is termed as nucleosome.

Chromosome and Chromatid facebook group and then go to file section
1. The most condensed (compact) form of the chromatin is the chromosome.

2. The double stranded DNA helix in each chromosome has a length that is thousand
times the diameter of the nucleus.
3. 1 chromosome consists of 2 chromatides. The 2 chromatides attach to each-other
at the centromere of the chromosome.
Vandana Janghel, Asst. Professor, SVITS, BSP, (C.G.)

facebook group and then go to file section
4. Proteins that attach to the centromere are called kinetochores. Microtubules of the
mitotic spindle-apparatus bind to kinetochores.
Kinetochore
5.
Chromatid
Centromere
6. The ends of the chromosome arms are the telomeres.

7. The number of the chromosomes is different in various species. For example
humans have 46 consist of 22 pair’s autosomes and 2 sex chromosomes, dogs
have 78, and cats have 38. “Solution-Pharmacy” believes in SHARING, not in selling
Karyotype
1. In human autosomal chromosomes are present in two identical copies
2. Normal karyotypes for women contain two X chromosomes and are denoted 46,
XX
3. Normal karyotypes for men have both an X and a Y chromosome denoted 46, XY.
Diploid cell
Sexually reproducing species have somatic cells (body cells), which are diploid [2n]
having two sets of chromosomes. “Solution-Pharmacy” believes in SHARING, not in selling
Haploid Cells
1. Gametes, reproductive cells (egg, sperm), are haploid [n], they have one set of
chromosomes.
2. Gametes are produced by meiosis of a diploid germ line cell.
3. When a male and a female gamete merge (fertilization), a new diploid cell
(fertilized egg) is formed. From this cell a new organism develops.
Chemical composition of the Chromatin

1. Histone + nonhistone proteins
2. RNA : mRNA, tRNA, rRNA and the own RNAs of the nucleus (e.g. snRNA)
3. Ions (Mg2+, Ca2+, etc.)
4. Chemical modification of histones→structural changes of chromatin (e.g.
condensation or loosening)
5. Nonhistone proteins: e.g. structural proteins, transport proteins, proteins
influencing transcription, protein and DNA chaperones


Deoxyribonucleic acid (DNA)
DNA is a polymer of Deoxyribonucleotide. DNA is composed of a phosphate-deoxyribose
sugar backbone and the nitrogenous bases adenine (A), guanine (G), cytosine (C) and
thymine (T). The monomeric deoxynucleotide in DNA are held together by 3’5’-
phosphodiester bridge.
Figure1: Deoxynucleotide
Structure of DNA
1. Watson and Crick proposed DNA double helix structure with two
polydeoxyribonucleotide chain (strand) chains.
2. The two strands are antiparallel. 5’→ 3′ orientation of one and 3’ → 5’orientation of
the other.
3. Diameter of double helix is 20 Ao (2nm).
4. The average distance between two adjacent base pairs is about 3.4 Ao (0.34 nm).
5. Each turn is 34 Ao (3.4 nm) with 10 pairs of nucleotides.
6. Phosphodiester linkages form the sugar-phosphate backbone of DNA.
7. The two chains are complementary to each other, purine of one chain pairs with
pyrimidine of the other.
8. Adenine pairs with thymine (A-T) has 2 hydrogen bond (A=T) and guanine pairs
with cytosine (G-C) has 3 hydrogen bond.
9. Complementary base pairing proves the Chargaff rule that A = T and С = G.
10. The genetic information stored in one of the two strands known as template strand.
Figure 2: (A) Watson-Crick model of DNAVandana

helix (B)Janghel, Asst. Professor,
Complementary SVITS,
base pairing in BSP,
DNA(C.G.)
helix
Functions of DNA
1. Genetic Information (Genetic Blue Print) for cell. DNA is responsible for the
inheritance and transmission of specific characteristics from one generation to the
other.
2. Replication DNA has unique property of replication or production of carbon copies
3. Chromosomes DNA occurs inside chromosomes. This is essential for equitable
distribution of DNA during cell division.
4. Recombination’s During meiosis, crossing over gives rise to new combination of
genes called recombinations.
5. Mutations Mutations are the factor responsible for all variations and evolution.
6. Transcription DNA gives rise to RNAs through the process of transcription.
7. Cellular Metabolism synthesis of specific proteins, enzymes and hormones through
the help of specific RNAs.
8. Differentiation “Solution-Pharmacy” believes in SHARING, not in selling
9. DNA Finger Printing You can download all of our uploaded study materials by joining our "Solution-Pharmacy"
10. Gene Therapy
Ribonucleic acid (RNA)
RNA is a polymer of ribonucleotides are held together by 3’5’- phosphodiester bridge. RNA
is composed of a phosphate-ribose sugar backbone and the nitrogenous bases adenine (A),
guanine (G), cytosine (C) and uracil (U).
Size
RNA molecule is much smaller in size than DNA. It consists of up to 12,000 nucleotides.
Types
There are three types of RNA molecules, each having a specific function:
1. Messenger RNA (m-RNA)

2. Ribosomal RNA (r-RNA) Available on- YouTube-Facebook (Group and Page) & Instagram
3. Transfer RNA (t-RNA) facebook group and then go to file section
1. Messenger RNA (mRNA)

Function: Messenger RNA is translated to form proteins
2. Transfer RNA (tRNA):
Function: Brings amino acids to ribosomes during translation of mRNA in protein
synthesis.

tRNA Amino acid attachment site
Complementary base pair Acceptor arm
T ΨC arm
D arm
Variable arm
Anticodon arm
mRNa
Codon
Figure 3: Structure of mRNA and tRNA

3. Ribosomal RNA (rRNA) is a component of ribosomes involved in protein synthesis.
Function of RNA
RNA is essential for the synthesis of proteins. Information contained within the genetic
code is typically passed from DNA to RNA to the resulting proteins.
Figure 1 : Central Dogma of life


Difference between DNA and RNA
Sr. no Parameter DNA RNA
Definition DNA is a polymer of Deoxyribo RNA is a polymer of ribonucleotides is
1 nucleotide held together by 3’5’- held together by 3’5’- phospho-diester
phosphodiester bridge. bridge.
2 Strand Double stranded helix structure Single stranded polynucleotide
3 Pentose Sugar Deoxyribose Ribose
4 Pyrimidine Thymine and cytosine Uracil and cytosine
5 Chargaff’s rule Obey rule, A=T and C=G Not obeyed
6 Alkali hydrolysis Cannot be hydrolysed Hydrolyze to to 2’3’-cylclic diester
7 Orcinol colour Cannot be identified Cannot be identified
reaction


GENETIC CODE
Code words for amino acid
Definition: Genetic code is the three nucleotide (triplet) base sequences in mRNA that act as
code word for amino acids in protein synthesis. The genetic words are called codon.
Description of Genetic code “Solution-Pharmacy” believes in SHARING, not in selling

1. Genetic code presented in mRNA.
2. Four nucleotide base are used to form codon
Purine – Adenine (A) and Guanine (G)
Pyrimidine – Cytosine (C) and Uracil (U)
3. The nucleotide sequence written from 5’ end to 3’ end.
4. 64 codon (43) are formed of different combination of 3 bases.
5. 61 codon code for 20 amino acid found in proteins. Three codon UAA, UGA, UAG are
termination codon don’t code for amino acid, act as stop signal in protein synthesis.
6. AUG and GUG are chain initiating codon.
Characteristics of Genetic code YouTube Link- https://www.youtube.com/c/SOLUTIONpushpendra
1. Universal
The same codon are used to code for same amino acid in all living organism.
E.g. AUG for methionine
Exception: AUA code for Isoleucine in cytoplasm and methionine in mitochondria
2. Specific
A particular codon always codes for the same amino acid
E.g. UGG is codon for tryptophan
3. Non overlapping
All codon are independent set of 3 bases. There is no overlapping
4. Commaless
It is commaless and without punctuation. Genetic is read from a fixed starting point as a
continuous sequence of base taken three at a time.
E.g. UUUCUUAGAGGG is read as UUU/CUU/AGA/GGG
5. Degenerate YouTube Link- https://www.youtube.com/c/SOLUTIONpushpendra
Every amino acid has more than one codon except methionine.
E.g. AGU and AGC for serine and CUU, CUC, CUA, CUG for leucine
Vandana Janghel, Asst. Professor, SVITS, BSP 1

DNA Replication
DNA replication can be defined as a cellular process by which DNA makes a copy of itself
to produce identical daughter molecule of DNA, so that after division each cell contain a
complete complement of genetic material.
Semi conservative replication of DNA facebook group and then go to file section
The process of replication is semi conservative replication because the daughter DNA (new
synthesized DNA) has one half of the parental DNA and one half of newly synthesized DNA.
Original Parent DNA molecule
Daughter DNA contains one parent Daughter DNA contains second

strand and one newly synthesized parent strand and one newly
complimentary strand synthesized complimentary strand
Fig 1: Semi- conservative replication of DNA
Process of replication (3 steps)

I. Initiation Available on- YouTube-Facebook (Group and Page) & Instagram
II. Elongation You can download all of our uploaded study materials by joining our "Solution-Pharmacy"
III. Termination
I. Initiation
1. Initiation of DNA synthesis occurs at a specific site called origin of replication.
2. dna A, B & C protein binds to Ori.
3. Unwind or unzipping: Helicase seperates the two strand of DNA at origin of
replication.
4. Single stranded binding protein (SSB) binds to the separated single strand and
helps to stabilize the separated strand.
5. DNA gyrase (Topoisomerase 2) relieve the stress generated by helicase by
introducing negative supercoil.

II. Elongation
1. Synthesis of RNA primer by RNA primase & paired with template DNA strand.
2. DNA polymerase III adds deoxyribonucleotide to the RNA primer.
3. Two types of synthesis occur
a. Leading strand synthesis: Replicated in continues manner in 5’-3’ direction.
b. Lagging strand synthesis: The synthesis of DNA is discontinues. The small
fragements of the discontinuously synthesized DNA are called Okazaki
fragements which is synthesized in direction opposite to fork movement
4. Okazaki pieces are later joined to form continuous strand of DNA by DNA
polymerase 1 and DNA ligase. “Solution-Pharmacy” believes in SHARING, not in selling
III. Termination
1. The replication complex begins to remove the RNA primes by DNA polymerase I.
2. Gap left by their removal are filled up by proper base paired deoxyribonucleotide.
3. The new strand is proof read & after finding no mistake in the new DNA ligase seal
the fragment of newly synthesized DNA.
Fig 2: DNA replication

Transcription
Transription is a process of synthesis of Ribonucleic acid (RNA) from Deoxyribonucleic
acid.
Gene is functional unit of the DNA that can be transcribed. The genetic information stored in
DNA is passed onto RNA through transcription.
1. Template strand
DNA strand which serve as a template for RNA synthesis also called none coding or Antisense
strand.
2. Non template strand
Doesn’t participate in transcription also called coding strand or sense strand.
Fig 2: An overview of transcription
Stages of transcription “Solution-Pharmacy” believes in SHARING, not in selling

I. Formation of transcription complex
1. σ factor of RNA polymerase recognizes and the binds to specific region (sequence) on a
DNA known as promoter site.
2. RNA polymerase separates two strand of DNA locally.
II. Initiation
1. Core enzyme of RNA polymerase starts transcription at the separated DNA strand of
the initiation complex.
1. The first incoming NTP binds to RNA polymerase at start point of initiation site
(transcription site).

Fig 2: RNA polymerase of E. coli

III. Elongation
1. Sigma factor released & transcription proceeds from 5’ end to 3’ end antiparallel to the
DNA template.
2. RNA polymerase utilizes ribonucleotide triphosphate(ATP,GTP,CTP & UTP) for the
formation of RNA.
IV. Termination facebook group and then go to file section
The process of transcription stops by termination signal.

1. Rho dependent termination
Rho factor (specific protein) binds to the growing RNA and terminates transcription and
release RNA.
2. Rho independent termination
The termination is brought about by the formation of hairpins of newly synthesized
RNA.
Transcription in eukaryotes
Three types of RNA polymerase synthesize three different types of RNA.
Fig 3: An overview of Transcription in eukaryotes


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YouTube Link- https://www.youtube.com/c/SOLUTIONpushpendra YouTube Link- https://www.youtube.com/c/SOLUTIONpushpendra
You can download all of our uploaded study materials by joining our "Solution-Pharmacy" You can download all of our uploaded study materials by joining our "Solution-Pharmacy"
facebook group and then go to file section facebook group and then go to file section
Promoter site Transcription site Termination site
DNA template
Initiation
Newly synthesized RNA σ factor of RNA polymerase recognizes
the promoter site on DNA template strand
Termination
Binding of ρ factor to DNA or RNA
polymerase
ρ factor released and recycled σ factor released and recycled

Elongation
Elongation Addition of nucleoside
RNA chain growth triphosphate (ATP, GTP, UTP,
CTP) at transcription site

Elongation facebook group and then go to file section
RNA chain growth

Fig 3: Transcription (RNA synthesis)
Vandan Janghel, Assistant Professor, Bilaspur

PROTEIN SYNTHESIS (TRANSLATION)
Translation is the process of protein synthesis which involves the translation of nucleotide base
sequence of mRNA into the language of amino acid sequence.
Stages of protein synthesis

I. Requirement of the components
II. Activation of Amino acid Available on- YouTube-Facebook (Group and Page) & Instagram
III. Protein synthesis proper facebook group and then go to file section
IV. Chaperons and protein folding

V. Post translation modification
I. Components of protein synthesis

1. Amino acid
Out of 20 amino acids, half of them synthesized by the body (10 essential amino acid
provided through diet).
2. Ribosome
Ribosome is factory for protein synthesis. 70S for prokaryotes and 80S for eukaryotes
Ribosome found in association with rough endoplasmic reticulum
Functional ribosome consist of 2 subunit (one big and one small) and 3 sites
1. A site – Acceptor site (Aminoacyl tRNA binding site)
2. P site – Donor site (Peptidyl tRNA binding site)
3. E site – Exit site YouTube Link- https://www.youtube.com/c/SOLUTIONpushpendra
3. RNA
a. Messenger RNA (mRNA): Carry specific Information for protein synthesis
present on mRNA in the form of codon.
b. Transfer RNA (tRNA): Carry the amino acid to the growing peptide chain in
ribosome.
c. Ribosomal RNA (rRNA): For ribosome synthesis
4. Energy source: ATP and GTP
5. Protein factor: Needed for initiation, elongation and termination of protein synthesis.

II. Activation of Amino acid AA

E AMP
Aminoacyl tRNA synthetase (E)
Amino acids E-AMP-Amino acid
ATP PPi
tRNA
III. Protein synthesis proper: mRNA read in 5’ to 3’ direction. 3 steps

1. Initiation of translation
Recognition of initiation code, 5’ AUG is initiation codon. Require initiation factor
(EIF). Four steps
a. Ribosomal dissociation YouTube Link- https://www.youtube.com/c/SOLUTIONpushpendra
b. Formation of 43 S preinitiation complex
c. Formation of 48 S initiation complex
d. Formation of 80 S initiation complex
2. Elongation of translation
a. Binding of Aminoacyl tRNa to A site
The 80S initiation complex contain methionine tRNA in the P site and A site is
free. Another Aminoacyl tRNA bind to the A site after proper codon
recognition on the RNa. Require Elongation factor EF-1α and GTP
b. Peptide bond formation
Peptidyl tranferase enzyme catalyses formation of peptide bond
c. Translocation
Growing pepetide chain move from A site to P site. Require EF-1 and GTP.
Deacylated tRNA moves to the E site from where it leaves the ribosome
3. Termination
After several cycle of elongation of peptide chain one of the stop codon or
termination codon (UAA, UAG, and UCA) terminates growing peptide chain.
Release factor (eRF) recognizes stop signal. eRF-GTP complex in association of
enzyme Pepetidyl tranferase cleaves peptide bond between polypeptide and the tRNA
occupying P site.

Translocation
Another aminoacyl tRNA

attached to A site after
Met codon recognition.
Step 1, 2, 3 repeated until

peptide chain is complete
80S initiation complex

Aminoacyl tRNA
Met
Met
Termination codon
Peptidyl transferase
(Peptide bond formation)
Met
Peptide synthesized
m RNA
Inhibitors of Protein synthesis

Antibiotics are the substances produced by bacteria of fungi which inhibit the growth of other
organism. Majority of Antibiotics inhibit bacterial protein synthesis.
Sr. no. Antibiotics Inhibition mechanism
1 Streptomycin Inhibit the initiation of protein synthesis
2 Tetracycline Inhibit binding of Aminoacyl tRNA to ribosomal complex
3 Puromycin Inhibit protein synthesis by incorporating in growing peptide
chain by attachment through A site
4 Chloramphenicol Inhibit elongation by inhibiting peptidyl tranferase
5 Erythromycin Binds to 50S subunit of bacterial ribosome and inhibit
translocation.


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ORGANIZATION OF MAMMALIAN GENOME

Organization of Eukaryotic DNA

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1. The most condensed (compact) form of the chromatin is the chromosome.

Vandana Janghel, Asst. Professor, SVITS, BSP, (C.G.)

6. The ends of the chromosome arms are the telomeres.

Chemical composition of the Chromatin

“Solution-Pharmacy” believes in SHARING, not in selling

Vandana Janghel, Asst. Professor, SVITS, BSP, (C.G.)

Figure 2: (A) Watson-Crick model of DNAVandana

Ribonucleic acid (RNA)

1. Messenger RNA (m-RNA)

1. Messenger RNA (mRNA)

Vandana Janghel, Asst. Professor, SVITS, BSP, (C.G.)

tRNA Amino acid attachment site

Complementary base pair Acceptor arm

Figure 3: Structure of mRNA and tRNA

3. Ribosomal RNA (rRNA) is a component of ribosomes involved in protein synthesis.

Figure 1 : Central Dogma of life

“Solution-Pharmacy” believes in SHARING, not in selling

Vandana Janghel, Asst. Professor, SVITS, BSP, (C.G.)

Difference between DNA and RNA

Sr. no Parameter DNA RNA

Definition DNA is a polymer of Deoxyribo RNA is a polymer of ribonucleotides is

1 nucleotide held together by 3’5’- held together by 3’5’- phospho-diester

phosphodiester bridge. bridge.

2 Strand Double stranded helix structure Single stranded polynucleotide

3 Pentose Sugar Deoxyribose Ribose

4 Pyrimidine Thymine and cytosine Uracil and cytosine

5 Chargaff’s rule Obey rule, A=T and C=G Not obeyed

6 Alkali hydrolysis Cannot be hydrolysed Hydrolyze to to 2’3’-cylclic diester

7 Orcinol colour Cannot be identified Cannot be identified

“Solution-Pharmacy” believes in SHARING, not in selling

Vandana Janghel, Asst. Professor, SVITS, BSP, (C.G.)

Description of Genetic code “Solution-Pharmacy” believes in SHARING, not in selling

Vandana Janghel, Asst. Professor, SVITS, BSP 1

Original Parent DNA molecule

Daughter DNA contains one parent Daughter DNA contains second

Fig 1: Semi- conservative replication of DNA

Process of replication (3 steps)

Vandana Janghel, Asst. Professor, SVITS, BSP 1

Fig 2: DNA replication

Vandana Janghel, Asst. Professor, SVITS, BSP 2

Fig 2: An overview of transcription

Stages of transcription “Solution-Pharmacy” believes in SHARING, not in selling

“Solution-Pharmacy” believes in SHARING, not in selling

Fig 2: RNA polymerase of E. coli

Vandana Janghel, Asst. Professor, SVITS, BSP 3

The process of transcription stops by termination signal.

Fig 3: An overview of Transcription in eukaryotes

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Vandana Janghel, Asst. Professor, SVITS, BSP 4

Promoter site Transcription site Termination site

ρ factor released and recycled σ factor released and recycled

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RNA chain growth

Vandan Janghel, Assistant Professor, Bilaspur

Stages of protein synthesis

IV. Chaperons and protein folding

I. Components of protein synthesis

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II. Activation of Amino acid AA