Lecture 1 - Organization of DNA – Prokaryotes, Eukaryotes, Viruses & organelle DNA-Mitochondria and | Molecular Biology (DNA) by ILLL, DU - Biotechnology Engineering (BT) PDF Download

 Page 1


 
1 
Institute of Lifelong Learning, University of Delhi 
 
 
 
Molecular Biology 
Lesson: Organization of DNA – Prokaryotes, Eukaryotes, 
Viruses 
& Organelle DNA – Mitochondria and Chloroplast DNA 
Lesson Developer: Dr. Shailly Anand 
College/Dept: Molecular Biology Laboratory, Department 
of Zoology, University of Delhi 
 
 
 
 
 
 
 
 
 
 
 
 
 
Page 2


 
1 
Institute of Lifelong Learning, University of Delhi 
 
 
 
Molecular Biology 
Lesson: Organization of DNA – Prokaryotes, Eukaryotes, 
Viruses 
& Organelle DNA – Mitochondria and Chloroplast DNA 
Lesson Developer: Dr. Shailly Anand 
College/Dept: Molecular Biology Laboratory, Department 
of Zoology, University of Delhi 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
2 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
Table of Contents 
Chapter: Organization of DNA (Prokaryotes, Eukaryotes 
and Viruses) & Organelle DNA  
? Introduction  
? Organization of DNA in Prokaryotes 
? General overview 
? Gene Structure 
 
? Organization of DNA in Eukaryotes 
? General overview 
? Gene Structure 
? Packaging of DNA 
? Histone proteins 
? Nucleosome (10nm) 
? 30nm fibre 
? Loops (300nm) 
? Chromosome (1400nm) 
? Organization of DNA in Viruses 
? RNA viruses 
? (+) sense strand viruses 
? (-) sense strand viruses 
? DNA viruses 
? Small DNA viruses 
? Large DNA viruses 
? Segmented or multipartite viruses 
 
? Organelle DNA 
 
? Mitochondrial DNA (mtDNA) 
? Chloroplast DNA 
? Endosymbiotic theory 
 
? Summary  
? Practice Questions 
? Glossary 
? References 
Page 3


 
1 
Institute of Lifelong Learning, University of Delhi 
 
 
 
Molecular Biology 
Lesson: Organization of DNA – Prokaryotes, Eukaryotes, 
Viruses 
& Organelle DNA – Mitochondria and Chloroplast DNA 
Lesson Developer: Dr. Shailly Anand 
College/Dept: Molecular Biology Laboratory, Department 
of Zoology, University of Delhi 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
2 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
Table of Contents 
Chapter: Organization of DNA (Prokaryotes, Eukaryotes 
and Viruses) & Organelle DNA  
? Introduction  
? Organization of DNA in Prokaryotes 
? General overview 
? Gene Structure 
 
? Organization of DNA in Eukaryotes 
? General overview 
? Gene Structure 
? Packaging of DNA 
? Histone proteins 
? Nucleosome (10nm) 
? 30nm fibre 
? Loops (300nm) 
? Chromosome (1400nm) 
? Organization of DNA in Viruses 
? RNA viruses 
? (+) sense strand viruses 
? (-) sense strand viruses 
? DNA viruses 
? Small DNA viruses 
? Large DNA viruses 
? Segmented or multipartite viruses 
 
? Organelle DNA 
 
? Mitochondrial DNA (mtDNA) 
? Chloroplast DNA 
? Endosymbiotic theory 
 
? Summary  
? Practice Questions 
? Glossary 
? References 
 
3 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
Introduction 
Ever since the discovery of DNA as the genetic material, its double helical structure, 
composition and alongside historic inventions like Sanger?s method of DNA sequencing, high 
resolution microscopy and other molecular tools, a lot has been revealed. In recent years, 
as genome sequencing projects have gained momentum, a vast pool of information has 
accumulated. This has provided a new dimension to the existing knowledge of the makeup 
of chromosomal DNA. This in turn has helped scientists to correlate the changes in the 
organization of DNA with respect to increase in complexity of the organism.  
The story begins with the origin of life on earth making it a living planet. It has been 
hypothesized that life originated in an RNA world and in order to attain stability it gave rise 
to DNA. The primitive unicellular organisms changed to multi-cellular forms and eventually 
to higher organisms with extensive cell differentiation. Keeping pace with these changes, 
the DNA too underwent enormous changes the result of which can be seen as the difference 
in the organization pattern in prokaryotes to eukaryotes and viruses.  
We are aware of all the basic differences between the prokaryotes and the eukaryotes. 
Prokaryotes are unicellular and lack any membrane bound organelles like the nucleus, 
mitochondria, chloroplast, lysosome etc. while eukaryotes on the other hand have well 
defined membrane bound organelles each with its distinct structure and function. In addition 
to the chromosomal DNA, eukaryotes contain organelle DNA in the mitochondria (in animal 
cells) and chloroplast (in plant cells). Prokaryotes also contain extrachromosomal DNA but 
in the form of plasmids that replicate within the same cell. Apart from these differences, 
their genetic makeup (i.e. organization) of DNA also differs (Table 1). This chapter thus 
focuses on all these aspects giving a clearer view of the chromosomal sequence and 
diversity in nature. 
 
Organization of DNA in Prokaryotes 
General overview 
Prokaryotic cells like Escherichia coli generally have a singular circular DNA but recent 
research has shown the presence of even multiple and linear forms of DNA. Apart from 
being relatively smaller in size, they lack any membrane bound nucleus. The distinct 
region in the cell where the DNA remains packaged is known as the nucleoid. When the 
circular DNA undergoes replication, it forms two entangled daughter DNA molecules which 
are separated by a specific class of topoisomerase enzyme known as DNA gyrase. The 
newly synthesized DNA also does not face the problem of end- replication as in eukaryotes 
which will be discussed in the next section. As mentioned before, prokaryotes often harbor 
plasmids which are extrachromosomal, self replicating DNA molecules and may be present 
in single to multiple copies. They carry genes that may provide its host cell with specific 
traits like resistance to antibiotics, tolerance to xenobiotics etc. 
Page 4


 
1 
Institute of Lifelong Learning, University of Delhi 
 
 
 
Molecular Biology 
Lesson: Organization of DNA – Prokaryotes, Eukaryotes, 
Viruses 
& Organelle DNA – Mitochondria and Chloroplast DNA 
Lesson Developer: Dr. Shailly Anand 
College/Dept: Molecular Biology Laboratory, Department 
of Zoology, University of Delhi 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
2 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
Table of Contents 
Chapter: Organization of DNA (Prokaryotes, Eukaryotes 
and Viruses) & Organelle DNA  
? Introduction  
? Organization of DNA in Prokaryotes 
? General overview 
? Gene Structure 
 
? Organization of DNA in Eukaryotes 
? General overview 
? Gene Structure 
? Packaging of DNA 
? Histone proteins 
? Nucleosome (10nm) 
? 30nm fibre 
? Loops (300nm) 
? Chromosome (1400nm) 
? Organization of DNA in Viruses 
? RNA viruses 
? (+) sense strand viruses 
? (-) sense strand viruses 
? DNA viruses 
? Small DNA viruses 
? Large DNA viruses 
? Segmented or multipartite viruses 
 
? Organelle DNA 
 
? Mitochondrial DNA (mtDNA) 
? Chloroplast DNA 
? Endosymbiotic theory 
 
? Summary  
? Practice Questions 
? Glossary 
? References 
 
3 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
Introduction 
Ever since the discovery of DNA as the genetic material, its double helical structure, 
composition and alongside historic inventions like Sanger?s method of DNA sequencing, high 
resolution microscopy and other molecular tools, a lot has been revealed. In recent years, 
as genome sequencing projects have gained momentum, a vast pool of information has 
accumulated. This has provided a new dimension to the existing knowledge of the makeup 
of chromosomal DNA. This in turn has helped scientists to correlate the changes in the 
organization of DNA with respect to increase in complexity of the organism.  
The story begins with the origin of life on earth making it a living planet. It has been 
hypothesized that life originated in an RNA world and in order to attain stability it gave rise 
to DNA. The primitive unicellular organisms changed to multi-cellular forms and eventually 
to higher organisms with extensive cell differentiation. Keeping pace with these changes, 
the DNA too underwent enormous changes the result of which can be seen as the difference 
in the organization pattern in prokaryotes to eukaryotes and viruses.  
We are aware of all the basic differences between the prokaryotes and the eukaryotes. 
Prokaryotes are unicellular and lack any membrane bound organelles like the nucleus, 
mitochondria, chloroplast, lysosome etc. while eukaryotes on the other hand have well 
defined membrane bound organelles each with its distinct structure and function. In addition 
to the chromosomal DNA, eukaryotes contain organelle DNA in the mitochondria (in animal 
cells) and chloroplast (in plant cells). Prokaryotes also contain extrachromosomal DNA but 
in the form of plasmids that replicate within the same cell. Apart from these differences, 
their genetic makeup (i.e. organization) of DNA also differs (Table 1). This chapter thus 
focuses on all these aspects giving a clearer view of the chromosomal sequence and 
diversity in nature. 
 
Organization of DNA in Prokaryotes 
General overview 
Prokaryotic cells like Escherichia coli generally have a singular circular DNA but recent 
research has shown the presence of even multiple and linear forms of DNA. Apart from 
being relatively smaller in size, they lack any membrane bound nucleus. The distinct 
region in the cell where the DNA remains packaged is known as the nucleoid. When the 
circular DNA undergoes replication, it forms two entangled daughter DNA molecules which 
are separated by a specific class of topoisomerase enzyme known as DNA gyrase. The 
newly synthesized DNA also does not face the problem of end- replication as in eukaryotes 
which will be discussed in the next section. As mentioned before, prokaryotes often harbor 
plasmids which are extrachromosomal, self replicating DNA molecules and may be present 
in single to multiple copies. They carry genes that may provide its host cell with specific 
traits like resistance to antibiotics, tolerance to xenobiotics etc. 
 
4 
Institute of Lifelong Learning, University of Delhi 
Genome size defined as the DNA length of one haploid 
set of chromosome also varies greatly in prokaryotes 
and eukaryotes. As the organism complexity 
increases, the number of proteins that it synthesizes 
also increases. Moreover, cell specialization results in 
only specific proteins being expressed in specific cells 
only. Hence the genome size can be correlated with 
the DNA complexity. It is due to this reason that 
prokaryotes have a smaller genome size (ranging from 
10
4
 and 10
7
bp) compared to the eukaryotes (size 
ranging from 10
8 
to 10
11
). But as more and more 
genomes have been sequenced and their gene content 
is evaluated, it negates the correlation between the 
genome size and complexity. Rather than the genome 
size, it is now evident that the gene content or the 
number of genes can be correlated with the 
complexity of DNA. As a result, scientists have 
compared the genome size of different organisms with 
respect to the number of proteins it synthesizes and 
this resulted in a new term called “Gene density”. 
Gene density can be defined as the average number of 
genes per million base pairs of DNA. The 4.5 Mbp 
genome of E. coli when studied showed that it 
comprises almost entirely of genes (~ 4400) except 
for a small region called Ori which does not code for any protein but marks the site for 
origin of replication. The gene density has been calculated to be 950. Human on the other 
hand have nearly 10 folds lower (9.3) gene density. Similar correlations have been drawn 
for many other sequenced genomes. All the results have shown an inverse correlation 
between the gene density and organism complexity. The more complex the organism, 
the lower is its gene density while the simpler the organism, the higher is its gene density. 
Prokaryotes being less complex than eukaryotes, therefore have a high gene density than 
that in eukaryotes. This relation now raises yet another query – What causes the gene 
density to be higher in prokaryotes? 
This can be attributed to the fact that in case of prokaryotes, the non- coding regions, also 
called as the intergenic DNA sequences (DNA sequence in between the genes; introns) is 
rare. It also lacks in the presence of repetitive DNA and even if present, it is in negligible 
number. Moreover, prokaryotes are polycistronic, i.e., multiple genes are present in a 
single transcript under the control of a single promoter. Due to these reasons, the 
prokaryotic DNA comprises of overlapping genes, and thus yielding a higher gene density.    
It is important to note that unlike eukaryotes, the DNA in prokaryotes is not associated with 
histone proteins, it is rather condensed by certain other packaging proteins. Prokaryotic 
genomes also contain a single Origin of replication. The chromosomes lack centromeres 
and telomeres which represent the heterochromatic regions in the eukaryotic chromosomes. 
The process by which the chromosome duplicates and segregates is still poorly understood. 
It neither has a cell cycle with distinct phases nor does it have any checkpoints. 
 
Gene Structure 
‘C-value paradox’ or the 
‘C-value enigma’. . . 
„C? stands for the content of 
DNA. It is expected that the 
more complex an organism is, 
the more amount of DNA it 
should have and vice-versa. 
This shows that the two should 
have a linear relationship. 
Therefore, many organisms 
were studied and the number of 
proteins coded by the genome 
was compared to the increase in 
the genome size. It was found 
that even for slight increase in 
number, the genome increased 
by many folds. Thus the DNA 
content was not the parameter 
to know the complexity of the 
organism. What was believed 
was not true – but a paradox! 
Page 5


 
1 
Institute of Lifelong Learning, University of Delhi 
 
 
 
Molecular Biology 
Lesson: Organization of DNA – Prokaryotes, Eukaryotes, 
Viruses 
& Organelle DNA – Mitochondria and Chloroplast DNA 
Lesson Developer: Dr. Shailly Anand 
College/Dept: Molecular Biology Laboratory, Department 
of Zoology, University of Delhi 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
2 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
Table of Contents 
Chapter: Organization of DNA (Prokaryotes, Eukaryotes 
and Viruses) & Organelle DNA  
? Introduction  
? Organization of DNA in Prokaryotes 
? General overview 
? Gene Structure 
 
? Organization of DNA in Eukaryotes 
? General overview 
? Gene Structure 
? Packaging of DNA 
? Histone proteins 
? Nucleosome (10nm) 
? 30nm fibre 
? Loops (300nm) 
? Chromosome (1400nm) 
? Organization of DNA in Viruses 
? RNA viruses 
? (+) sense strand viruses 
? (-) sense strand viruses 
? DNA viruses 
? Small DNA viruses 
? Large DNA viruses 
? Segmented or multipartite viruses 
 
? Organelle DNA 
 
? Mitochondrial DNA (mtDNA) 
? Chloroplast DNA 
? Endosymbiotic theory 
 
? Summary  
? Practice Questions 
? Glossary 
? References 
 
3 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
Introduction 
Ever since the discovery of DNA as the genetic material, its double helical structure, 
composition and alongside historic inventions like Sanger?s method of DNA sequencing, high 
resolution microscopy and other molecular tools, a lot has been revealed. In recent years, 
as genome sequencing projects have gained momentum, a vast pool of information has 
accumulated. This has provided a new dimension to the existing knowledge of the makeup 
of chromosomal DNA. This in turn has helped scientists to correlate the changes in the 
organization of DNA with respect to increase in complexity of the organism.  
The story begins with the origin of life on earth making it a living planet. It has been 
hypothesized that life originated in an RNA world and in order to attain stability it gave rise 
to DNA. The primitive unicellular organisms changed to multi-cellular forms and eventually 
to higher organisms with extensive cell differentiation. Keeping pace with these changes, 
the DNA too underwent enormous changes the result of which can be seen as the difference 
in the organization pattern in prokaryotes to eukaryotes and viruses.  
We are aware of all the basic differences between the prokaryotes and the eukaryotes. 
Prokaryotes are unicellular and lack any membrane bound organelles like the nucleus, 
mitochondria, chloroplast, lysosome etc. while eukaryotes on the other hand have well 
defined membrane bound organelles each with its distinct structure and function. In addition 
to the chromosomal DNA, eukaryotes contain organelle DNA in the mitochondria (in animal 
cells) and chloroplast (in plant cells). Prokaryotes also contain extrachromosomal DNA but 
in the form of plasmids that replicate within the same cell. Apart from these differences, 
their genetic makeup (i.e. organization) of DNA also differs (Table 1). This chapter thus 
focuses on all these aspects giving a clearer view of the chromosomal sequence and 
diversity in nature. 
 
Organization of DNA in Prokaryotes 
General overview 
Prokaryotic cells like Escherichia coli generally have a singular circular DNA but recent 
research has shown the presence of even multiple and linear forms of DNA. Apart from 
being relatively smaller in size, they lack any membrane bound nucleus. The distinct 
region in the cell where the DNA remains packaged is known as the nucleoid. When the 
circular DNA undergoes replication, it forms two entangled daughter DNA molecules which 
are separated by a specific class of topoisomerase enzyme known as DNA gyrase. The 
newly synthesized DNA also does not face the problem of end- replication as in eukaryotes 
which will be discussed in the next section. As mentioned before, prokaryotes often harbor 
plasmids which are extrachromosomal, self replicating DNA molecules and may be present 
in single to multiple copies. They carry genes that may provide its host cell with specific 
traits like resistance to antibiotics, tolerance to xenobiotics etc. 
 
4 
Institute of Lifelong Learning, University of Delhi 
Genome size defined as the DNA length of one haploid 
set of chromosome also varies greatly in prokaryotes 
and eukaryotes. As the organism complexity 
increases, the number of proteins that it synthesizes 
also increases. Moreover, cell specialization results in 
only specific proteins being expressed in specific cells 
only. Hence the genome size can be correlated with 
the DNA complexity. It is due to this reason that 
prokaryotes have a smaller genome size (ranging from 
10
4
 and 10
7
bp) compared to the eukaryotes (size 
ranging from 10
8 
to 10
11
). But as more and more 
genomes have been sequenced and their gene content 
is evaluated, it negates the correlation between the 
genome size and complexity. Rather than the genome 
size, it is now evident that the gene content or the 
number of genes can be correlated with the 
complexity of DNA. As a result, scientists have 
compared the genome size of different organisms with 
respect to the number of proteins it synthesizes and 
this resulted in a new term called “Gene density”. 
Gene density can be defined as the average number of 
genes per million base pairs of DNA. The 4.5 Mbp 
genome of E. coli when studied showed that it 
comprises almost entirely of genes (~ 4400) except 
for a small region called Ori which does not code for any protein but marks the site for 
origin of replication. The gene density has been calculated to be 950. Human on the other 
hand have nearly 10 folds lower (9.3) gene density. Similar correlations have been drawn 
for many other sequenced genomes. All the results have shown an inverse correlation 
between the gene density and organism complexity. The more complex the organism, 
the lower is its gene density while the simpler the organism, the higher is its gene density. 
Prokaryotes being less complex than eukaryotes, therefore have a high gene density than 
that in eukaryotes. This relation now raises yet another query – What causes the gene 
density to be higher in prokaryotes? 
This can be attributed to the fact that in case of prokaryotes, the non- coding regions, also 
called as the intergenic DNA sequences (DNA sequence in between the genes; introns) is 
rare. It also lacks in the presence of repetitive DNA and even if present, it is in negligible 
number. Moreover, prokaryotes are polycistronic, i.e., multiple genes are present in a 
single transcript under the control of a single promoter. Due to these reasons, the 
prokaryotic DNA comprises of overlapping genes, and thus yielding a higher gene density.    
It is important to note that unlike eukaryotes, the DNA in prokaryotes is not associated with 
histone proteins, it is rather condensed by certain other packaging proteins. Prokaryotic 
genomes also contain a single Origin of replication. The chromosomes lack centromeres 
and telomeres which represent the heterochromatic regions in the eukaryotic chromosomes. 
The process by which the chromosome duplicates and segregates is still poorly understood. 
It neither has a cell cycle with distinct phases nor does it have any checkpoints. 
 
Gene Structure 
‘C-value paradox’ or the 
‘C-value enigma’. . . 
„C? stands for the content of 
DNA. It is expected that the 
more complex an organism is, 
the more amount of DNA it 
should have and vice-versa. 
This shows that the two should 
have a linear relationship. 
Therefore, many organisms 
were studied and the number of 
proteins coded by the genome 
was compared to the increase in 
the genome size. It was found 
that even for slight increase in 
number, the genome increased 
by many folds. Thus the DNA 
content was not the parameter 
to know the complexity of the 
organism. What was believed 
was not true – but a paradox! 
 
5 
Institute of Lifelong Learning, University of Delhi 
If one considers the gene structure in prokaryotes, it comprises a promoter region, the gene 
(or genes in case of operons) followed by a terminator region. The promoter lies upstream 
of the gene and has two main sites at -10 and -35bp positions. The former contains the 
TATAAT sequence where the RNA polymerase binds and opens the doubles stranded DNA 
for transcription to initiate while the later contains TTGACA sequence and serves as the 
RNA polymerase recognition site. Only a single type of RNA polymerase is present that 
forms the transcript. The mRNA thus formed by transcription is short lived and stays for 
only a few minutes after it is synthesized. Therefore, transcription is always coupled with 
translation and does not take place in different regions of the cell (Fig. 1). For translation, 
the initiator tRNA is N-formylated methionine (fMet). This describes the general 
organization of DNA in prokaryotes. Detailed view of the gene structure and regulation will 
be covered in subsequent chapters separately. 
 
 
Figure 1: Gene structure in prokaryotes. Multiple genes are under the control of the same 
promoter (Polycistronic). The promoter contains two distinct regions – RNA polymerase 
recognition site (-35bp) and RNA polymerase binding site (-10bp). Transcription is coupled 
with translation and produces proteins. The mRNA is short lived due to absence of any 
modifications. 
Source: Author 
 
Organization of DNA in Eukaryotes