Paper

GENOME ORGANIZATION IN BIOTECHNOLOGY

ORGANISASI GENOM DALAM BIOTEKNOLOGI

Lecturer : Dr. Syahmi Edi, M. Si

Arranged by :

Akehke Rezekine Meidea Naosis

4213141028

Biology Education Study Program 2021

FACULTY OF MATHEMATICS AND NATURAL SCIENCES

UNIVERSITAS NEGERI MEDAN 2024

 CHAPTER I

PRELIMINARY
1.1 Background
Perhaps the first multidisciplinary science was biotechnology, which uses biological
systems or their byproducts to produce goods and services. The rapidly growing field of
biotechnology has broadened to encompass novel approaches to gather and evaluate data
regarding the composition and operations of genomes, which, in conjunction with
environmental factors, govern every facet of development and growth via genomics.
Significant progress has also been achieved in the field of genome editing, enabling the
precise and innovative manipulation of genome structures. The first instances of three-parent
babies have increased the use of biotechnology most recently. These developments offer until
unheard-of chances to learn more about gene transfer, epigenetics, and genomic structure.
Future biotechnology applications will expand upon the advances made in genomics and
genome editing to encompass a wider range of sub-sectors. This will necessitate intricate
contributions from a variety of fields, including bioinformatics, microbial genetics,
agricultural science, and human reproductive physiology (Gartland, et al., 2017).

Studying the nucleic acids (DNA and RNA) that control gene expression in all organisms
has led to the rise of genomic sciences as one of the biotechnology industry's fastest-growing
sectors. In traditional genetics, genetic regions associated with the breeder's objective were
chosen for gene-modifying operations. Afterwards, researchers employed chemical and
radiation mutagens to enhance the likelihood of genetic mutations in test organisms. These
techniques were costly and time-consuming, despite their usefulness. Reverse genetics, on the
other hand, moves in the opposite direction of classical genetics' so-called forward genetic
screens. Reverse genetics is a molecular genetics technique that examines the phenotypic
consequences of particular modified gene sequences in order to shed light on a gene's
function (Khalil, 2020).

The rapid development of genetic engineering require us to comprehend the concept of

genome therefore this paper is made to risen our insight about the concept of genome and the
role of genome in biotechnology

1.2 Problem Formulation

1. What is a genome
2. What is the difference between genome & gene?
3. What is a chromosome?
4. How is the viral genome?
5. How is the prokaryote genome?
6. How is the eukaryote genome?
7. How is the flow of genetic information?
8. What is the role of genome in biotechnology?

1.3 Objectives
1. The comprehend the definition of genome
2. To comprehend the difference between genome and gene
3. To comprehend what a chromosome is
4. To comprehend the viral genome
5. To comprehend the prokaryote genome
6. To comprehend the eukaryote genome
7. To comprehend how the genetic information flow
8. To comprehend the role of genome in biotechnology
 TABLE OF CONTENTS

CHAPTER I ............................................................................................................................... 2
PRELIMINARY ........................................................................................................................ 2
1.1 Background ................................................................................................................. 2
1.2 Problem Formulation................................................................................................... 2
1.3 Objectives .................................................................................................................... 2
TABLE OF CONTENTS ........................................................................................................... 4
CHAPTER II.............................................................................................................................. 5
CONTENT ................................................................................................................................. 5
2.1 Definition of Genome ...................................................................................................... 5
2.2 Concept of Genome & Gene ............................................................................................ 5
2.3 Chromosome .................................................................................................................... 6
2.4 Viral Genome ................................................................................................................... 7
2.5 Prokaryote Genome ......................................................................................................... 9
2.6 Eukaryote Genome......................................................................................................... 12
2.7 Flow of Genetic Information ......................................................................................... 13
CHAPTER III .......................................................................................................................... 18
CLOSING ................................................................................................................................ 18
3.1 Conclusion................................................................................................................. 18
3.2 Suggestion ................................................................................................................. 18
REFERENCES ........................................................................................................................ 19
 CHAPTER II

CONTENT
2.1 Definition of Genome
According to Nair (2008), Genome is a complete genetic or DNA complement of an
organism, it includes the genetic material of the nucleus and cytoplasm.

According to Goldman & Landweber (2016), the genome is often described as the
information repository of an organism. Whether millions or billions of letters of DNA, its
transmission across generations confers the principal medium for inheritance of organismal
traits.

According to Blundell (2006), the genome is the complete set of instructions for
making an organism. The term "genome" refers to an organism's set of genes and
chromosomes.

According to those definitions above, we can conclude that genome is a complete

genetic material of an organism that includes the genetic material in the nucleus and the
mitochondria which is an instruction for making an organism and transmitted across
generations.

2.2 Concept of Genome & Gene

According to Mustami & Muthiadin (2021), Genes are parts of DNA that code for
proteins our bodies need to function. According to Ayala in Nusantari (2014), Genes are
segments of DNA from one DNA to another DNA. In the DNA molecule there are genes, in
this case a gene is a certain sequence of nucleotides from DNA that expresses certain
characteristics which codes for the formation of a polypeptide, which codes for the formation
of an RNA or which is needed for the transcription of another gene. The concept of genes
developed after Mendel's discovery of segregation and independent selection. Initially, genes
were thought to have several special characteristics, namely: (1) a hereditary unit that was
inherited from generation to generation, (2) a functional unit that produced a phenotype; (3) a
functional aspect that causes its own duplication. According to Nair (2008), A gene is defined
as a segment of DNA molecule (A DNA molecule = a chromosome), which carries all the
biochemical information of a polypeptide or RNA molecule, along with its regulatory
elements.

According to Mahner & Kary (1997), The genome is: (a) the set of genes of an
organism ; (b) the set of genes of a cell; (c) the set of genes of a gamete; (d) a set of
chromosomes; and (e) the set of genes contained in a haploid chromosome set of a eukaryotic
cell. According to Nair (2008), Genome is a complete genetic or DNA complement of an
organism, it includes the genetic material of the nucleus and cytoplasm.

We can conclude that genome is a complete set of gene and gene is a certain sequence
of DNA molecule that carried information.
2.3 Chromosome
According to Hartono & Azimata (2019), Chromosomes are chromatin that close
together, shorten and enlarge during the division process in the cell nucleus (nucleus), so that
their parts can be seen clearly under an ordinary microscope. Chromosome comes from the
words chroma = color, and soma = body. Found in the plasma nucleus, in the form of objects
that are straight like rods or bent, and consist of materials that easily bind dyes. The term
chromosome was first introduced by W. Waldeyer in 1888, although Flemming (1879) had
seen chromosome division in the cell nucleus. The expert who first suspected that these
objects were involved in the mechanism of heredity was Roux (1887) who reported that the
number of these objects in the nucleus of different creatures was different, and the amount
remained constant throughout life. Meanwhile, the classical principles of genetics are the
deductive thoughts of Gregor Mendel in 1865 which many people ignored until 1902, Walter
Sutton and Theodor Boveri discovered similarities between the behavior of chromosomes
during meiosis and Mendel's laws and drew the conclusion that chromosomes are gene
carriers. Morgan (1993), discovered the function of chromosomes in the transfer of genetic
traits. Several other experts, such as Heitz (1935), Kuwanda (1939), Gritter (1940) and
Kauffmann (1948), then provided more information about chromosome morphology.

On a macroscopic scale, bacterial chromosomes are either circular or linear. Circular

chromosomes are most common, at least among the best-studied bacteria. Eukaryotic
chromosomes are invariably linear, and they have two ends, each carrying a special structure
called a telomere, and a organized region called the centromere which allows the
chromosome to attach to cellular machinery that moves it to the proper place during cell
division (Higgins, 2001).

Chromosomes consist of alternating dark and light parts. The dark part is called the
Heterochromatin area, which is a fold of nucleoprotein that is very dense and stacked. By
coloring, the stacked part will absorb the red color so it looks thick and short. The light part is
called the Euchromatin area: the nucleoprotein folds but is not as dense as the dark part. The
nucleotide coils in interphase are mostly open (stretched) so that the chromosomes appear
long and slender. In the prophase the folded coils appear thick and short (Nusantari, 2014).
 Almost all mammals have between 18 and 30 nuclear chromosomes occurring in
single copies (haploid state, n) in their eggs and sperm (gametes). With fertilization of the egg
by the sperm, these two haploid genomes combine, and in mammals proceed to yield two
copies of each chromosome per cell (diploid state, 2n). The number of chromosomes varies
across mammalian and primate species, but is almost always the same within species
(Klegarth & Eisenberg, 2018).

2.4 Viral Genome

Viruses are non-living particles that must infect and subvert cellular machinery of a
host to reproduce. Viruses consist of a protein coat and a core that contains the genome. Even
though the genomes of viruses are the most simplest and smallest, they are the most diverse
due to diverse evolutionary histories as well as diversity in strategies for packing genome in a
coat. It can be made of single-stranded DNA (ssDNA), double-stranded DNA (dsDNA),
single-stranded RNA (ssRNA), or even double-stranded RNA (dsRNA). These molecules of
nucleic acids may be linear or circular. The complete nucleotide sequences of many viral
genomes have been determined (Nair, 2008)
 The viral genome is packed inside a symmetric protein capsid, composed of either a
single or multiple proteins, each of them is encoding a single viral gene. Due to this
symmetric structure, viruses could encode all the necessary information for constructing a
large capsid using a small set of genes. A capsid along with the enclosed nucleic acid is called
a nucleocapsid. In enveloped viruses, the nucleocapsid is surrounded by a lipid bilayer and is
studded with a layer of glycoproteins. Often, the nucleic acid is associated with a protein
called nucleoprotein (Chaitanya, 2019)

Viral genomes are very small, have little intergenic space, and few genes (herpes virus
contains ~200 genes, and many others have far fewer genes). There are various types of
viruses. Although they have a protein coat around their hereditary material, they lack
properties of cells such as membranes, ribosomes, enzymes, and ATP synthesis ability. Thus,
they can only proliferate using a host cell’s translational machinery. In other words, they are
obligate intracellular parasites. Their replication cycle consists of attachment and entry into
the cell; replication of viral nucleic acid; synthesis of viral proteins; and finally, assembly of
viral components and escape from host cells. Bacteriophages have received the greatest
attention from molecular geneticists. A bacteriophage is a virus that infects bacteria only
(Nair, 2008)

Viruses are broadly divided into DNA viruses and RNA viruses. Both DNA and RNA
viruses can either single stranded or double stranded, with a circular, linear or segmented
arrangement. DNA and RNA viruses are distinguished by their features, such as monopartite
or multipartite. In monopartite, their genome is having a single nucleic acid molecule. All
double stranded DNA genomes contain only a single nucleic acid molecule and few of the
viruses with single stranded genomes are reported to have multiple segments. In contrast,
RNA viral genomes are generally multipartite, with more frequency for single stranded RNA
viruses. Additionally, single stranded virus genomes may be either positive sense (+) where
the RNA present in the genome will of the same polarity as mRNA and will encode the genes
or negative sense (-), where the entire ssRNA genome must be copied and the copied strand is
transcribed. Some single stranded viruses are ambisense (a mixture of + and - sense)
(Chaitanya, 2019).
 Bacteriophages have a simple structure, which consists of their double-stranded DNA
(in some cases single stranded, e.g., M13) surrounded by a protein coat. Only the DNA enters
into the bacteria. Integration is achieved by recombination between a 15 bp sequence called
att (for attachment) in the host chromosome and an identical sequence in the phage
chromosome. This recombination requires an integrase (Int) enzyme encoded by the phage.
Bacteriophages are used for gene cloning in molecular biology. DNA fragments can be
inserted into a phage and following transfection of competent bacteria, many copies of the
desired DNA fragment can be obtained (Nair, 2008).

2.5 Prokaryote Genome

In prokaryotes, genome size is relatively small, but bigger than that of a virus. There
is considerable variation in the size among prokaryotes and in some cases the genome is
bigger than certain eukaryotic cells. For example, the genome size of bacillus megasterium is
30 Mb and that of yeast is 12.1 Mb, which is the same as a eukaryote. The genome sizes in
other bacteria are smaller than this. In most cases, the genome consists of a single circular
chromosome, but there are exceptions. They also possess small independently replicating,
circular, double-stranded DNA molecules known as plasmids. Plasmids can be 1 to 300 kb
long and may exist as multiple, free copies. They also carry genes, which are absent in
bacterial chromosome (Nair, 2008).

Generally, the bacterial genome has a high gene density (i.e., genes are close together)
with very small intergenic regions. Unlike eukaryotic systems, the major part of the genome
is functional. About 85 to 90% of total DNA is involved in protein coding, about 20-10% is
the intergenic DNA, and less than 2% of DNA is made up of transposable elements.
Functionally related genes located together as a group called operons and introns are
extremely rare. Overlapping genes are also common in bacterium as in the case of viruses.
Bacterial genomes have associated proteins, used to pack it into a nucleoid, but the proteins
are not similar to the histones of eukaryotes.
 In Brown (2002), some features of prokaryote genome are

• It contains more genes than the human segment. This region of yeast
chromosome III contains 26 genes thought to code for proteins and two that code for transfer
RNAs (tRNAs), short non-coding RNA molecules involved in reading the genetic code
during protein synthesis.

• Relatively few of the yeast genes are discontinuous. In this segment of

chromosome III none of the genes are discontinuous. In the entire yeast genome there are
only 239 introns, compared with over 300 000 in the human genome.

• There are fewer genome-wide repeats. This part of chromosome III contains a
single long terminal repeat (LTR) element, called Ty2, and four truncated LTR elements
called delta sequences. These five genome-wide repeats make up 13.5% of the 50-kb
segment, but this figure is not entirely typical of the yeast genome as a whole. When all 16
yeast chromosomes are considered, the total amount of sequence taken up by genome-wide
repeats is only 3.4% of the total. In humans, the genome-wide repeats make up 44% of the
genome.
 In e. coli, 4,639 kb DNA contains about 2,400 genes, which make up about 80% of
the total DNA. The remaining 20% is made up of intergenic regions. There are three cases of
overlapping genes and about 27% of the transcriptional units are organized into 75
polycistronic groups or operons. The genes in an operon are functionally related. (In Aquifex
aeolicus, operon genes are not functionaly related as per our ideas about operons.) Another
example, methanococcus jannaschii, is an extreme thermophilic bacteria that has three
circular chromosomes; one 166 Mb, plus two smaller ones of 58.4 and 16.5 kb. The entire
genome was sequenced in 1996; 58% of its genes do not match any known genes. The
majority of genes involved in energy production, cell division, and general metabolism, more
closely resemble eubacterial genes. They have some similarities with that of eukaryotic genes
involved in RNA synthesis, protein synthesis, and DNA synthesis. They contain histone
genes and DNA organized into chromatin, and introns in tRNA genes (Nair, 2008)
2.6 Eukaryote Genome
Eukaryotic genomes are much more complex than bacterial genomes. They cover an
enormous size range (more than three orders of magnitude) and display different levels of
structural complexity.

There are two types of genomes in a eukaryotic system. They are nuclear genomes
and cytoplasmic genomes. Cytoplasmic genomes include mitochondrial genomes in the case
of animals and both mitochondrial and chloroplast genomes in the case of plants. For
example, the human genome, the term used to describe the total genetic information (DNA
content) in human cells, consists of two genomes: a complex nuclear genome, which
accounts for 99.9995% of the total genetic information, and a simple mitochondrial genome,
which accounts for the remaining 0.0005% (Nair, 2008).

Most of bacterial genomes are circular, while all eukaryotic genomes so far known are
linear (here organelle genomes are not considered). The main reason for a large genome size
in eukaryotes is the existence of many repeat sequences, which are minority in prokaryotes.
Pseudogenes and introns are also few in prokaryotic genomes, while both are abundant in
eukaryotic genomes. High occurrences of gene duplications in eukaryotes prompted
production of many pseudogenes. Horizontal gene transfers are known to be quite frequent in
prokaryotes, and they are rare in eukaryotes. Finally, genome duplications sometimes occur
in eukaryotes, especially in plants and in vertebrates, but genome duplication is so far not
known for prokaryotic genomes (Saitou, 2013)
2.7 Flow of Genetic Information
A. REPLCATION

The Watson and Crick model predicts that when the double helix replicates, each of
the two daughter molecules contains one old strand, which came from the parent molecule,
and one newly created strand. The semi-conservative model can be distinguished from the
conservative replication model, which states that the two parent strands come back together
after the process (that is, the parent molecule will be conserved). In the third model, called
the dispersive model, the four strands of DNA that exist after replication are a mixture of old
and new DNA. Although the mechanisms for conservative or dispersive DNA replication are
not easily determined, these models remain likely to be correct until proven wrong. After two
years of initial research in the late 1950s, Matthew Meselson and Franklin Stahl designed an
ingenious experiment that differentiated the three models. Their experiment supports the
semiconservative model of DNA replication, as predicted by Watson and Crick, and is widely
known among biologists as a classic example of elegant experimental design (Nugroho &
Rahayu, 2018)

According to Simion (2018),DNA replication process includes:

1. Initiation

For a cell to divide, it must first replicate its DNA.This process is initiated at
particular points in the DNA, known as “origins”, which are targeted by initiator proteins. In
E. coli this protein is DNA; in yeast, this is the origin recognition complex.Sequences used by
initiator proteins tend to be “AT-rich” (rich in adenine and thymine bases), because A-T base
pairs have two hydrogen bonds (rather than the three formed in a C-G pair) which are easier
to unzip.Once the origin has been located, these initiators recruit other proteins and form the
pre-replication complex, which unzips the double-stranded DNA.

2. Elongation

DNA polymerase has 5’-3’ activity. All known DNA replication systems require a free 3’
hydroxyl group before synthesis can be initiated (Important note: DNA is read in 3’ to 5’
direction where as a new strand is synthesized in the 5’ to 3’ direction—this is often
confused). Four distinct mechanisms for initiation of synthesis are recognized. These are :
 i. All cellular life forms and many DNA viruses, phages and plasmids use a primase
to synthesize a short RNA primer with a free 3’ OH group which is subsequently
elongated by a DNA polymerase.
ii. The retro elements (including retroviruses) employ a transfer RNA that primes
DNA replication by providing a free 3′ OH that is used for elongation by the
reverse transcriptase.
iii. In the adenoviruses and the φ29 family of bacteriophages, the 3’ OH group is
provided by the side chain of an amino acid of the genome attached protein (the
terminal protein) to which nucleotides are added by the DNA polymerase to form
a new strand.
iv. In the single stranded DNA viruses- a group that includes the circo viruses, the
geminiviruses, the parvoviruses and others and the many phages and plasmids that
use the rolling circle replication (RCR) mechanism, the RCR endonuclease creates
a nick in the genome strand (single stranded viruses) or one of the DNA strands
(plasmids). The 5′ end of the nicked strand is transferred to a tyrosine residue on
the nuclease and the free 3′ OH group is then used by the DNA polymerase to
synthesize the new strand.
3. Termination

Termination requires that the progress of the DNA replication fork must stop or be
blocked. Termination at a specific locus, when it occurs, involves the interaction between two
components:

i. A termination site sequence in the DNA, and

ii. A protein which binds to this sequence to physically stop DNA replication.
 B. TRANSCRIPTION

Transcription is the synthesis of RNA under the direction of DNA. Both nucleic acids
speak the same language, and information is simply transcribed, or copied, from one
molecule to another. Apart from being a template for the synthesis of new complementary
strands during DNA replication, DNA strands can also act as templates for assembling
complementary RNA nucleotide sequences. For protein-coding genes, the resulting RNA
molecule is an accurate transcription of the protein-building instructions contained in the
gene, much like a college transcript is an accurate record of your grades. Like your transcript,
the transcript RNA molecule can be sent in many copies. This type of RNA molecule is called
messenger RNA (messenger RNA, mRNA) because it contains genetic messages from DNA
to the cell's protein-synthesizing mechanisms. (transcription is a general term for the
synthesis of any type of RNA with a DNA template) (Nugroho & Rahayu, 2018).
 C. TRANSLATION

Translation. is the synthesis of polypeptides, which occurs under the direction of

mRNA. During this stage, language changes occur. Cells must translate the base sequence of
the mRNA molecule into the amino acid sequence of the polypeptide. The site of translation
is the ribosome (ribosome), a complex of particles that facilitates the orderly linking of amino
acids into a polypeptide chain. Transcription and translation occur in all organisms. There are
three domains of living things: Bacteria, Archae, and Eukarya. Organisms in the first two
domains are grouped as prokaryotes because bacterial and archaeal cells lack the membrane-
enclosed nucleus that defines eukaryotic cells. Most research on transcription and translation
has been carried out on bacteria and eukaryotes (Nugroho & Rahayu, 2018).
 CHAPTER III

CLOSING
3.1 Conclusion
In conclusion, the genome plays a pivotal role in biotechnology, serving as the
foundation for understanding, manipulating, and harnessing the capabilities of living
organisms. From gene identification and genetic engineering to drug discovery, diagnostics,
and bioproduction, genomic information drives innovation across various fields, ultimately
shaping the future of healthcare, agriculture, industry, and environmental sustainability. As
technology advances and our understanding of the genome deepens, the potential for
biotechnology to address complex challenges and improve human well-being continues to
expand.

3.2 Suggestion
To increase our insight about modern biotechnology we require to comprehend about
genome so writer encourage all of us to update to the current literature
 REFERENCES

Blundell, R., 2006. What is Genomics. Research Journal of Biological Sciences, 1(4), pp. 40-
42.

Brown, T. A., 2002. GENOMES. 2nd ed. s.l.:Garland Science.

Chaitanya, K. V., 2019. Genome & Genomics. s.l.:Springer Nature Singapore Pte Ltd.

Gartland, K. M. A. et al., 2017. Advances in biotechnology: Genomics and genome editing.

The EuroBiotech Journa, 1(1), pp. 3-10.

Goldman, A. D. & Landweber, L. F., 2016. What Is a Genome?. PLOS GENETICS, 12(7).

Hartono, R. & Azimata, R., 2019. BIOLOGI SEL DAN GENETIKA. s.l.:KEMENTERIAN
KESEHATAN REPUBLIK INDONESIA.

Higgins, N. P., 2001. Chromosome structure. In: ENCYCLOPEDIA OF LIFE SCIENCES.

s.l.:Macmillan Publishers Ltd, Nature Publishing Group, pp. 1-10.

Khalil, A. M., 2020. The genome editing revolution: review. Journal of Genetic Engineering
and Biotechnology, 18(68).

Klegarth, A. R. & Eisenberg, D. T. A., 2018. Chromosome. In: W. Trevathan, ed. The
International Encyclopedia of Biological Anthropology. s.l.:John Wiley & Sons, Inc,
pp. 1-4.

Mahner, M. & Kary, M., 1997. What exactly are genomes, genotypes, and phenotypes? And
what about phenomes?. J. Theor. Biol., pp. 55-63.

Mustami, M. K. & Muthiadin, C., 2021. KONSEP DASAR PEWARISAN GEN PADA
MANUSIA. Gowa: Alauddin University Press.

Nair, A. J., 2008. Introduction to Biotechnology and Genetic Engineering. 3rd ed. New Delhi:
Laxmi Publications Pvt Limited.

Nugroho, E. D. & Rahayu, D. A., 2018. Pengantar Bioteknologi: Teori dan Aplikasi.
Yogyakarta: Deepublish.

Nusantari, E., 2014. Genetika. Yogyakarta: Deepublish.

Saitou, N., 2013. Eukaryote Genomes. Introduction to Evolutionary Genomics, Volume 17,
pp. 193-222.

Simion, T., 2018. DNA Replication. Current Trends in Biomedical Engineering &
Biosciences, 16(4), pp. 1-7.