MAKALAH BIOLOGI MOLEKULER
UJIAN TENGAH SEMESTER
Nama: Sarah Ananta
NPM: 1806148593
Program Studi Teknik Kimia
Departemen Teknik Kimia
Fakultas Teknik
Universitas Indonesia
Depok, 2020
Kata Pengantar
Pendahuluan
Coronaviruses are enveloped viruses containing the largest reported RNA genomes. As a result of their
pleomorphic nature, our structural insight into the coronavirion is still rudimentary, and it is based
mainly on 2D electron microscopy. Here we report the 3D virion structure of coronaviruses obtained by
cryo-electron tomography. Our study focused primarily on the coronavirus prototype murine hepatitis
virus (MHV). MHV particles have a distinctly spherical shape and a relatively homogenous size (≈85 nm
envelope diameter). The viral envelope exhibits an unusual thickness (7.8 ± 0.7 nm), almost twice that of
a typical biological membrane. Focal pairs revealed the existence of an extra internal layer, most likely
formed by the C-terminal domains of the major envelope protein M. In the interior of the particles,
coiled structures and tubular shapes are observed, consistent with a helical nucleocapsid model. Our
reconstructions provide no evidence of a shelled core. Instead, the ribonucleoprotein seems to be
extensively folded onto itself, assuming a compact structure that tends to closely follow the envelope at
a distance of ≈4 nm. Focal contact points and thread-like densities connecting the envelope and the
ribonucleoprotein are revealed in the tomograms. Transmissible gastroenteritis coronavirion
tomograms confirm all the general features and global architecture observed for MHV. We propose a
general model for the structure of the coronavirion in which our own and published observations are
combined.
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that
project from their surface, an unusually large RNA genome, and a unique replication strategy.
Coronaviruses cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs
and upper respiratory disease chickens to potentially lethal human respiratory infections. Here we
provide a brief introduction to coronaviruses discussing their replication and pathogenicity, and current
prevention and treatment strategies. We will also discuss the outbreaks of the highly pathogenic Severe
Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the recently identified Middle Eastern
Respiratory Syndrome Coronavirus (MERS-CoV).
Recently, a novel coronavirus (2019-nCoV), officially known as severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in China. Despite
drastic containment measures, the spread of this virus is ongoing. SARS-CoV-
2 is the aetiological agent of coronavirus disease 2019 (COVID-19)
characterised by pulmonary infection in humans. The efforts of international
health authorities have since focused on rapid diagnosis and isolation of
patients as well as the search for therapies able to counter the most severe
effects of the disease. In the absence of a known efficient therapy and because
of the situation of a public-health emergency, it made sense to investigate the
possible effect of chloroquine/hydroxychloroquine against SARS-CoV-2 since
this molecule was previously described as a potent inhibitor of most
coronaviruses, including SARS-CoV-1. Preliminary trials of chloroquine
repurposing in the treatment of COVID-19 in China have been encouraging,
leading to several new trials. Here we discuss the possible mechanisms of
chloroquine interference with the SARS-CoV-2 replication cycle.
1. Penyebab penyakit Covid-19
2. Penjelasan mengenai Struktur virus penyebab Covid-19, bagaimana para peneliti
melihat struktur virus tersebut.
3. Penjelasan mengenai Sekuens dari asam nukleat virus penyebab Covid-19,
bagaimana para peneliti menentukan sekues tersebut (SK. 1)
4. Protein-protein yang telah diketahui sekuens dan strukturnya dari virus penyebab
Covid19, Bagaimana para peneliti menentukan strukturnya. (SK. 2)
5. Perkembangan alat diagnostic penyakit Covid-19 beserta prinsip kerjanya. (SK. 1
dan 2)
2. Coronaviruses, a genus within the Coronaviridae family (order Nidovirales- see
Box 1), are pleomorphic, enveloped viruses. The viral membrane contains the
transmembrane (M) glycoprotein, spike (S) glycoprotein, and envelope (E)
protein and surrounds a disordered or flexible, likely helical nucleocapsid 2,
Barcena M, et al. Cryo-electron tomography of mouse hepatitis virus: Insights into the structure
of the coronavirion. Proc Natl Acad Sci U S A. 2009;106:582–7. This paper and ref 3
use novel methodologies to obtain detailed models of the structure of the intact coronavirion.
[PMC free article] [PubMed] [Google Scholar
Coronaviruses, genus dalam keluarga Coronaviridae (orde
Nidovirales- lihat Kotak 1), adalah virus pleomorfik,
terselubung. Selaput virus mengandung transmembran (M)
glikoprotein, spike (S) glikoprotein, dan protein amplop (E) dan
mengelilingi protein nukleokapsid heliks yang helai atau
fleksibel, kemungkinan heliks 2,
By contrast, three weeks after the first known case of the disease now known as COVID-
19, China had notified the WHO of a spike in cases of a pneumonia-like disease. Two
weeks after that, the coronavirus had been isolated, genetically sequenced, and a
diagnostic test developed, giving China the tools it needed to launch one of the greatest
infectious-disease containment efforts the world has ever seen.
The COVID-19 virus, although not as lethal as SARS, has proved much more pervasive.
It took less than two months from the discovery of the first infection for the number of
confirmed cases to pass the total that SARS reached over several months. And in three
months, COVID-19 has killed more than five times as many people as SARS.
Scientists in China have sequenced the genome of the COVID-19 virus demonstrating that it is
a completely new virus, albeit closely related to the coronavirus (CoV) responsible for severe
acute respiratory syndrome (SARS). Their findings are published in the journal Chinese Medical
Journal. Read more from Asian Scientist Magazine at:
https://www.asianscientist.com/2020/02/topnews/china-coronavirus-covid-19-study/
In the present study, researchers led by Dr. Wang Jianwei at the Chinese Academy of Medical
Sciences, Institute of Pathogen Biology, China, used next generation sequencing (NGS) to
definitively identify the pathogen causing illness in Wuhan. They focused on five patients
admitted to Jin Yin-tan Hospital in Wuhan, most of whom were workers in the Huanan Seafood
Market in Wuhan. Read more from Asian Scientist Magazine at:
https://www.asianscientist.com/2020/02/topnews/china-coronavirus-covid-19-study/
The researchers then constructed the whole genomic sequence of the new virus—now known
as COVID-19—and found that its genome sequence is 79 percent similar to the SARS-CoV,
about 51.8 percent similar to the MERS-CoV, and about 87.6-87.7 percent similar to other
SARS-like CoVs from Chinese horseshoe bats (called ZC45 and ZXC21). These findings clearly
suggest that the virus originated from bats. Read more from Asian Scientist Magazine at:
https://www.asianscientist.com/2020/02/topnews/china-coronavirus-covid-19-study/
1. Perkembangan alat diagnostic penyakit Covid-19 beserta prinsip kerjanya. (SK. 1
dan 2)
DEVICE DESCRIPTION AND TEST PRINCIPLE The COVID-19 RT-PCR Test is a real-time reverse
transcription polymerase chain reaction (rRT -PCR) test. The test uses three primer and probe
sets to detect three regions in the SARS-CoV-2 nucleocapsid (N) gene and one primer and
probe set to detect human RNase P (RP) in a clinical sample. RNA isolated from upper and
lower respiratory specimens (such as nasopharyngeal or oropharyngeal swabs, sputum, lower
respiratory tract aspirates, bronchoalveolar lavage, and nasopharyngeal wash/aspirate or
nasal aspirate) is reverse transcribed to cDNA and subsequently amplified using Applied
Biosystems QuantStudio7 Flex (QS7) instrument with software version 1.3. During the
amplification process, the probe anneals to a specific target sequence located between the
forward and reverse primers. During the extension phase of the PCR cycle, the 5’ nuclease
activity of Taq polymerase degrades the bound probe, causing the reporter dye (FAM) to
separate from the quencher dye (BHQ1), generating a fluorescent signal. Fluorescence
intensity is monitored at each PCR cycle by QS7.
1. RNA extraction
2. RNA was extracted from
clinical samples with the
3. MagNA Pure 96 system
(Roche, Penzberg,
Germany)
4. and from cell culture
supernatants with the viral
RNA
5. mini kit (QIAGEN, Hilden,
Germany).
6. RNA extraction
7. RNA was extracted from
clinical samples with the
8. MagNA Pure 96 system
(Roche, Penzberg,
Germany)
9. and from cell culture
supernatants with the viral
RNA
10. mini kit (QIAGEN, Hilden,
Germany).
11. RNA extraction
12. RNA was extracted from
clinical samples with the
13. MagNA Pure 96 system
(Roche, Penzberg,
Germany)
14. and from cell culture
supernatants with the viral
RNA
15. mini kit (QIAGEN, Hilden,
Germany).
1. RNA extraction
RNA was extracted from clinical samples with the
MagNA Pure 96 system (Roche, Penzberg, Germany)
and from cell culture supernatants with the viral RNA
mini kit (QIAGEN, Hilden, Germany).
2. Thermal cycling was
performed at 55 °C for
3. 10 min for reverse
transcription, followed by
95 °C for
4. 3 min and then 45 cycles
of 95 °C for 15 s, 58 °C for
30
5. s.
2. Thermal cycling was
performed at 55 °C for
3. 10 min for reverse
transcription, followed by 95
°C for
4. 3 min and then 45 cycles
of 95 °C for 15 s, 58 °C for
30
5. s.
Thermal cycling was
2.
performed at 55 °C for
10 min for reverse
transcription, followed by 95
°C for
3 min and then 45 cycles of 95
°C for 15 s, 58 °C for 30
s.
2. Thermal cycling was performed at 55 °C for
10 min for reverse transcription, followed by 95 °C for
3 min and then 45 cycles of 95 °C for 15 s, 58 °C for 30
s.
Conclusion
Over the past 50 years the emergence of many different coronaviruses that
cause a wide variety of human and veterinary diseases has occurred. It is
likely that these viruses will continue to emerge and to evolve and cause
both human and veterinary outbreaks owing to their ability to recombine,
mutate, and infect multiple species and cell types.
Future research on coronaviruses will continue to investigate many aspects
of viral replication and pathogenesis. First, understanding the propensity of
these viruses to jump between species, to establish infection in a new host,
and to identify significant reservoirs of coronaviruses will dramatically aid in
our ability to predict when and where potential epidemics may occur. As bats
seem to be a significant reservoir for these viruses, it will be interesting to
determine how they seem to avoid clinically evident disease and become
persistently infected. Second, many of the non-structural and accessory
proteins encoded by these viruses remain uncharacterized with no known
function, and it will be important to identify mechanisms of action for these
proteins as well as defining their role in viral replication and pathogenesis.
These studies should lead to a large increase in the number of suitable
therapeutic targets to combat infections. Furthermore, many of the unique
enzymes encoded by coronaviruses, such as ADP-ribose-1”-phosphatase, are
also present in higher eukaryotes, making their study relevant to
understanding general aspects of molecular biology and biochemistry. Third,
gaining a complete picture of the intricacies of the RTC will provide a
framework for understanding the unique RNA replication process used by
these viruses. Finally, defining the mechanism of how coronaviruses cause
disease and understanding the host immunopoathological response will
significantly improve our ability to design vaccines and reduce disease
burden.
