Group 6-3ebio: Assoc Prof. Loida R. Medina, PHD, RMT, Rmicro

ACTIVITY 1: INTRODUCTION TO THE CELL: CELLULAR STRUCTURE AND FUNCTION
GROUP 6- 3EBIO Assoc Prof. Loida R. Medina, PhD, RMT, RMicro

Miro, Raphael Christian S. BIO4212
Natividad, Ritchel Mae D. August 30, 2020
Noel, Reanna Rosary R.
Parojinog, Anne O.
ACTIVITY 1
Introduction to the Cell: Cellular Structure and function
1. What is the most conserved genome segment?

Upon searching for sequence similarities in the complete genomes of 13 organisms representing
disparate branches of the evolutionary tree of life, with the use of genome filtering method and MAVID
website, Isenbarger and his colleagues (2008) found that the ribosomal genes, namely the 16S and 23S
ribosomal RNA genes scored as the most highly conserved sequences (at highest scoring non- ribosomal
genetic regions scoring only 37 bits).The sequences identified within the 16S and 23S genes are known to
mediate several important interactions with transfer RNAs in the ribosome A, P, and E sites: with
elongation factors involved in translation; and between regions of the 30S and 50S subunits (Green and
Noller 1997; Yusupov et al. 2001).
2. What is the function of the proteins coded by these genes?

About 30 to 40 percent of these RNA segments are protein (Campbell, 2018). These compounds
bind to tRNAS as well as to other accessory molecules for protein synthesis, move along mRNA and
serve as catalysts in the assembly of amino acids (Lodish et al., 2000). The proteins that are coded by the
23s rRNA and 16s rRNA are associated with the L1 protein binding which primarily allows the L1
protein to be attached or in contact with the cytoskeleton of the cell (Bralant, 1981). The ribosomal
proteins are known for playing an essential role in ribosome assembly and protein translation as well as in
providing the structural framework for the 23S rRNA that actually carries out the peptidyltransferase
reaction (Bhagavan & Ha, 2015).
It is also found that these groups of proteins activate the tumor suppressor p53 pathway in
response to ribosomal stress. In addition, these ribosomal proteins are involved in various physiological
and pathological processes (Zhou et al., 2015). These proteins are generally located on the surface and
fill in the gaps and crevices of the folded RNA, and some contain globular domains on the ribosome
surface that send out extended regions of polypeptide chain that penetrate short distances into holes in the
RNA core. The main role of the ribosomal proteins seems to be to stabilize the RNA core, while
permitting the changes in rRNA conformation that are necessary for this RNA to catalyze efficient protein
synthesis (Alberts et al., 2002). In prokaryotes, the process of translation initiation is primarily promoted
by initiation proteins IF1, IF2, and IF3, which mediate base pairing of the initiator tRNA anticodon to the
mRNA initiation codon located in the ribosomal P-site. According to Jackson et al., (2010), eukaryotes
also have proteins that function in translation initiation, these organisms utilize proteins such as elF1,
elF2, elF3, elF4, and elF5.
3. Give examples of orthologs and paralogs.

In the human retina, according to Li (2006), the genes that codes the middle (OPN1MW gene)
and long-wave (OPN1LW gene) pigments, which are sensitive to green and red colors or the visible
wavelengths of these colors respectively, were first derived from duplication predating the existence of
humans. Despite the two being beside each other in the genome, these regions eventually diverged from
one another. Later, a divergence of the Old World (OW) monkey and human lineages took place yet the
OPN1MW and OPN1LW genes retained their function. As a result, it can be said that the OPN1MW and
BIO4212: ACTIVITY 01 MIRO, NATIVIDAD, NOEL, PAROJINOG:
3EBIO OPN1LW genes of humans are paralogous with one another while the human and OW monkey
OPN1MW gene, as well as the human and OW monkey OPN1LW genes are orthologous.
4. What are the causes of gene speciation and duplication?

As time passes by, Scientists discovered many mechanisms for the evolution of a new gene, one
of which is Duplication event in which it happens naturally all the time, it may be small, nucleotides long
or even an entire gene can be duplicated. From these duplicated genes, further mutations happen with
either a removal of nonfunctional genes or amplification of pre-existing genes.
Three examples of which are the gene duplication of FGF4 in a Dachshund DNA which gives this
dog species powerful legs for digging. This new DNA interacts with their growing bones, reshaping it and
gives rise to several new breeds. Another example is the diet of a Leaf-Eating Monkey which they
achieved by several factors and one of which is gene duplication of RNase1 found in blood, and in the
intestine; a protein once functioned with two separate jobs, was now duplicated to produce proteins with
different jobs. Lastly is the production of factor X (found also freely in blood) which functions to seal
wounds by initiating a series of chemical reactions resulting in a blood clot. Meanwhile the salivary
glands of venomous snake species are abundant with factor X proteins which when they inject into a prey,
will cause a rapid blood clot into the wound. The previous gene used for healing is now a deadly gene.
These examples of rapid mutation in specific parts of genes can ultimately lead to speciation.
5. Is gene speciation and duplication good or bad?

Gene speciation and duplication can either be beneficial or detrimental to the organism, or in the
same way it is to its environment and other organisms. Personally, I think it is neutral because, the
mutations happening in an organism for example an evolved prey to escape its predators, and to avoid
hunger, predators also adapt and evolve to the ways of its prey by different factors, and the cycle will go
on and on. Also it applies to the present times, as when viruses were discovered, humans made vaccines
to prevent the spread of viruses, and subsequently viruses also evolved to a more virulent type to avoid
the resistance given by the vaccines, and other drugs. So we cannot simply label gene speciation and
duplication as good or bad, but we can think of it as a natural thing to occur in this world.
6. What is the endosymbiotic theory?

Endosymbiotic theory is one of the proposed theories explaining the prokaryotic origin of the
eukaryotic cell, an idea rekindled by Lynn Margulis. Accordingly, a cell consumed another cell and let it
reproduce inside, giving an outcome of co-existence. The endosymbiosis involved at least an anaerobic
prokaryote host and an aerobic prokaryotic microbe which is the one being ingested. As the ingested cells
adapt inside its host cell, the mitochondria and chloroplasts are formed eventually (Gray, 2017 and Martin
et.al., 2015).
7. What are the evidence that eukaryotic cells evolved from bacterial cells?
It is to consider that there are more than one cell inside the host cell. Examples of endosymbiotic
relationships are amoeba and ciliates with their endosymbionts. As the endosymbiosis tooks place, the
evolutionary development of the mitochondrion came after. Cells possessing mitochondria can attain cell
3EBIO complexity using bioenergetic means (Journey to the Microcosmos, 2019 and Martin et.al., 2015).
Meanwhile, the photosynthetic prokaryotes, being able to produce their own DNA with their
chloroplasts, were said to have undergone independent symbiosis such as the Paramecium bursaria.
Through the course of time, the symbionts were inherited by the next generation and mutualism occurred
between them. (Journey to the Microcosmos, 2019; Martin et.al., 2015; and Gray, 2017).
References:
Journal Articles
Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York:
Garland Science; 2002. From RNA to Protein. Available from:
https://www.ncbi.nlm.nih.gov/books/NBK26829/
Bhagavan, N., & Ha, C. (2015). RNA and Protein Synthesis. Essentials of Medical Biochemistry, 419-
446. doi:10.1016/b978-0-12-416687-5.00023-3
Branlant, C., Krol, A., Machatt, M. A., Pouyet, J., Ebel, J., Edwards, K., & Kössel, H. (1981).
Primary and secondary structures of Escherichia coli MRE 600 23S ribosomal RNA.
Comparison with models of secondary structure for maize chloroplast 23S rRNA and for large
portions of mouse and human 16S mitochondrial rRNAs. Nucleic Acids Research, 9(17), 4303-
4324. doi:10.1093/nar/9.17.4303
Gray, M.W. (2017). Lynn Margulis and the endosymbiont hypothesis: 50 years later. Molecular Biology
of the Cell 28:1285-1287. DOI:10.1091/mbc.E16-07-0509
Green R, Noller HF (1997) Ribosomes and translation. Annu Rev Biochem 66:679–716.
10.1146/annurev.biochem.66.1.679
Isenbarger, T. A., Carr, C. E., Johnson, S. S., Finney, M., Church, G. M., Gilbert, W., Ruvkun, G. (2008).
The Most Conserved Genome Segments for Life Detection on Earth and Other Planets. Origins
of Life and Evolution of Biospheres, 38(6), 517-533. doi:10.1007/s11084-008-9148-z
Jackson, R., Hellen, C., Pestova, T. The mechanism of eukaryotic translation initiation and
principles of its regulation. Nat Rev Mol Cell Biol. 2010;11(2):113-127.
doi:10.1038/nrm2838
Li, W.-H. (2006). Homologous, Orthologous and Paralogous Genes. Encyclopedia of Life Sciences.
doi:10.1038/npg.els.0005297
Lodish, H., Berk, A., Zipursky, S. (2010).. Molecular Cell Biology. 4th edition. New York: W. H.
Freeman . Section 4.4, The Three Roles of RNA in Protein Synthesis.

3EBIO
Available from: https://www.ncbi.nlm.nih.gov/books/NBK21603/
Martin, W.F., Garg, S. & Zimorski, V. (2015). Endosymbiotic theories for Eukaryote origin.
Philosophical Transactions of the Royal Society B 370(1678): 20140330.
doi:10.1098/rstb.2014.0330.
Yusupov MM, Yusupova GZ, Baucom A, et al. Crystal structure of the ribosome at 5.5 A
resolution. Science. 2001;292(5518):883-896. doi:10.1126/science.1060089
Zhou, X., Liao, W., Liao, J., Liao, P., & Lu, H. (2015). Ribosomal proteins: Functions beyond the
ribosome. Journal of Molecular Cell Biology, 7(2), 92-104. doi:10.1093/jmcb/mjv014
Video
Journey to the Microcosmos (2019, July 23). Where did Eukaryote came from?- A Journey into
Endosymbiotic Theory. Youtube. https://www.youtube.com/watch?v=4LhBZ2H5SwM

3EBIO

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ACTIVITY 1: INTRODUCTION TO THE CELL: CELLULAR STRUCTURE AND FUNCTION

GROUP 6- 3EBIO Assoc Prof. Loida R. Medina, PhD, RMT, RMicro

1. What is the most conserved genome segment?

2. What is the function of the proteins coded by these genes?

3. Give examples of orthologs and paralogs.

4. What are the causes of gene speciation and duplication?

5. Is gene speciation and duplication good or bad?

6. What is the endosymbiotic theory?

BIO4212: ACTIVITY 01 MIRO, NATIVIDAD, NOEL, PAROJINOG:

BIO4212: ACTIVITY 01 MIRO, NATIVIDAD, NOEL, PAROJINOG:

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