My long journey

After the seventh week, i have complete my assignments which is create reflective journal using blog. For me, it was really interesting and amazing because we can have the chances doing something new especially as a students. I had never ever create a blog or something else which related to the journal. Through this reflective journal blog, I can increase my ability in writing and also in giving idea on something. I can write anything and give my opinions according what I had learned in class from week 1 until week 7. Next, I can create the possibility of making new realizations. I enjoyed creating this blog and start giving idea in blog although there were many allegation during finish this assignments. I remember in week 3, while I was doing my journal and suddenly my laptop shut down just like that so, all my works gone and I have not save my work yet. It was really sad and frustating because I must do this journal again start from the beginning. My laptop cannot function at all and I only depends my friend's laptop. Other than that, in week 4, I tried to connect this laptop to the wifi but it did not want to connect at all. I want to finish my reflective learning journal so I decided with my friends to stay at the cafe until our work done. We stay up late night at the cafe to finish up our assignments. This really give me new experiences because for the first time, I had never stay at cafe late night. Then after the 5 week, I really enjoyed doing this journal. I had many idea to write on the blog. After the lecture, usually I studied again in my room to understand and try to memorize what i had learned in the class so that I can continue create my journal according from my understanding. I can identify my strength and weakness in every topic. I spent time a lot of time to do this journal. Before start writing, I understand the topic first and sometimes I do the research to increase my general knowledge. Then, I search using google images to find the images that related to the topic to make it more clearly and of course to make it more interesting. So that I would not get bored to my reflective journal. I check many times until satisfied before publish the post. Sometimes if I have no idea to write about, I just stop and doing another work. Once I have an idea, immediately I continue my writing. This is really interesting because its like we were writing on our own diary. For sure not the diary about our life happening all the day but this is all about cellular and developmental biology topics. So, this is all my preparations and experiences during do this assignments. I hope this can enhance my learning experience and also can increase my understanding in this subject so I can perform well during my final examination.

The regulation of developmetantal and differentiation hormones

 In week 7, we were required to fill the teaching evaluation in the putrablast. We fill up the form and give the evaluation to the lecturers. After that, Dr Parameswari discussed the test 1 examination papers. We discussed the answer together the objective and the subjective questions. Through this, we can knew our mistake that we do during the test. Next, we learned about the plant growth regulators found in plants and explain their functions. Plant hormones are chemicals produced by plants that alter growth patterns and maintenance of the plant. Substance produced in a very low concentration and are mobile, both over short (diffusive) and long (mass-flow) distances. The plant hormones control cell activities by sending chemicals signals or messages to cells to do something or not to do the something, including activating the genes that code for specific enzymes or blocking gene transcription and plant hormones inhibit as well inhibit as promote cellular activities.

 
                                            Signal transduction in plants

After that, I had learned about hormones in plants. There are 5 classes of hormones in plants which are auxins, cytokinins, gibberillins, abscisic acid and lastly is ethylene. Auxins (plural of auxin /ˈɔːksɨn/) are a class of plant hormones (or plant growth substances) with some morphogen-like characteristics. Auxins have a cardinal role in coordination of many growth and behavioral processes in the plant's life cycle and are essential for plant body development. Auxins and their role in plant growth were first described by the Dutch scientist Frits Warmolt Went.^[1] Kenneth V. Thimann isolated this phytohormone and determined its chemical structure as indole-3-acetic acid (IAA). Went and Thimann co-authored a book on plant hormones, Phytohormones, in 1937. Auxin is increase the plasticity of plant cell walls and is involved in stem elongation. Auxin also enhances cell elongation.

                                                                                                                                                    auxin

    The main function of auxin is to help plants grow. Auxin stimulates plant cells to elongate, and the apical meristem of a plant is one of the main places that auxin is produced. This makes sense because the apical meristem is also the location that all the other parts of a plant grow from - the stem, leaves, and flowers.        

Then, I had read the lecture notes about phototropism. In phototropism, auxin migrates away from light. The stem will elongate faster on the extra auxin side.

                                                                                                         Phototropism

                                     
                                                               Gravitropism

Cytokines are a large group of proteins, peptides or glycoproteins that are secreted by specific cells of immune system. Cytokines are a category of signaling molecules that mediate and regulate immunity, inflammation and hematopoiesis. Cytokines are produced throughout the body by cells of diverse embryological origin. Cytokine is a general name; other names are defined based on their presumed function, cell of secretion, or target of action. For example, cytokines made by lymphocytes can also be referred to as lymphokines, while interleukins are made by one leukocyte and act on other leukocytes. And chemokines are cytokines with chemotactic activities. Cytokines may act on the cells that secrete them (autocrine action), on nearby cells (paracrine action), or in some instances on distant cells (endocrine action).

Cytokines generally function as intercellular messenger molecules that evoke particular biological activities after binding to a receptor on a responsive target cell.

                                                       Cytokinins

                                                                                               Auxin and Cytokinin interaction

Gibberellins are a group of plant hormones responsible for growth and development. Chemically speaking, gibberellins are actually acids. They are produced in the plastids of plant cells and are eventually transferred to the endoplasmic reticulum of the cell, where they are modified and prepared for use. Gibberellins are growth hormones that stimulate cell elongation and cause plants to grow taller. Gibberellins also have a role in other processes in plants, including stem elongation, germination, flowering, and fruit ripening. In humans, the pituitary gland secretes the human growth hormone at appropriate times; the plastids of a plant secrete gibberellin in a similar fashion. 

 Humans have glands that secrete hormones at different times to stimulate body processes such as growth, development, and the breaking down of sugars. Plants also have hormones that stimulate processes that are necessary for them to live. One hormone, abscisic acid, is involved in many developmental plant processes, including leaf abscission, responding to environmental stress, and inhibiting fruit ripening. Abscisic acid is produced in the roots of the plant as well as the terminal buds at the top of the plant. Abscisic acid is involved in several plant functions. Plants have openings on the bottom side of their leaves, known as stomata, that take in carbon dioxide and regulate water content. Abscisic acid has been found to function in the closing of these stomata during times when the plant does not require as much carbon dioxide or during drought times when the plant cannot afford to lose much water through transpiration. 

Ethylene is present in the tissues of ripening fruits, nodes of stems, senescent leaves, and flowers.

Functions of Ethylene

Leads to release of dormancy state
Stimulates shoot and root growth along with differentiation
Leaf and fruit abscission
Flower induction in Bromeliad
Stimulation of femaleness of dioecious flowers
Flower opening is stimulated
Flower and leaf senescence stimulation
Stimulation of Fruit ripening

After, i had learned about this, i knew the function of each every hormones. This topic is quite interesting because it is related in our daily life. Each hormones has their functions. I had found more interesting facts while I serching about all those 5 classes of hormones. Eventhough I did not like about the plants topic, but this topic has changed my perspective towards plants.

Pollination and development of plant embryo

    In week 6, we had learned about pollination and development of plant embryo. We were able to compare the development of animal and plant, explained the reproduction organ of plants and dicsuss zygotic and somatic embryogenesis. Dr. Parameswari had brought us two conical flasks containing the tissue culture plants. I was really excited to see the plant tissue culture becaue I had never seen these before in my real life. Dr. Parameswari tell us about her experience doing the tissue culture experiment. 

       Experiment of plant tissue culture

I had learned about the plants reproductive organ. I had learned this before during my matriculation session ad also during my high school. So this topic is quite similar for me. Dr. Parameswari explained us about the plants' reproductive organ which consist of anther, filament, stigma, style ovary, petal, ovule and sepal. Female reproductive organ of plants is stigma, style and ovary which is called as carpel. Male reproductive organ consists of anther and filament which is called as stamen.

                                                                                    

Plants' reproductive organ

After that, Dr. Parameswari had a quiz test on the subtopic we had learned. We required to answer it together in the class. After the quiz, I understand the topic directly because at that time, we tried to answer the question without referring the notes. Then, Dr.Parameswari explained us detail about the life cycle of angiosperm (flowering plants). She also show us the video about plants' reproductive organ so we can surely understand because we can imagined the structure in our mind. For me, the plants' reproductive organ is quite tough because we had never seen the process but during this lecture, i can imagine and understand what had Dr. Parameswari teach us because she always tells us to do the scl activity together in groups.



Life cycle of angiosperms (Flowering Plants)

Next, we also had discussed about double fertilization of plants. Pollination is the transfer of pollen to the part of a seed plant containing the ovules. Pollen eliminates the need for a film of water and can be dispersed great distances by air or animals. The other pollinating agent are winds, insects, animal and human. Then, if pollen germinates, it give rise to pollen tube that discharges two sperm into the female gametophyte within the ovule. One sperm nucleus fertilizes the egg, generating a 2N diploid zygote. Another sperm nucleus fertilizes a polar cell with two 1N nuclei, generating a 3N triploid endosperm which provides nutrients to the developing embryo. It was really amazing learn about the double fertilization of plants. It such a unique creation in life.

 

                                                 . Double fertilization

Furthermore, we also had discussed about the zygotic embryogenesis and somatic embryogenesis.  Plant embrogenesis is the process that produces a plant embryo from a fertilised ovule by assyetric cell division and the differentiation of undifferentiated cells into tissues and organs. it occures during sedd development. When the single-celled zygote undergoes a programmed pattern of cell division resulting in a mature embryo. Somatic embryos are formed from plant cells that are not normally involved the development of embryos and no endosperm or seed coat is formed around a somatic embryo.


                                Zygotic embyogenesis

Endosymbiotic theory

Next, we were required to answer the question before the lecture of new topic start. I knew a little bit about what does the endosymbiotic theory suggest and I can describe the structures, functions, and characteristics of the mitochondrion and chloroplast that have led scientists to propose the endosymbiotic theory. At the end of this lecture, we should able be able to describe the origin of mitochondria and chloroplast.

After had learned this topic, I had knew that the endosymbiosis theory suggest that eukaryotes arose from a symbiotic relationship between various prokaryotes, heterotrophic (aerobic) bacteria became mitochondria, cyanobacteria (photosynthetic) became chloroplasts and host cell was a large eukaryotic cell.





The origin of eukaryotic cell



Those are the evidence for symbiosis :

Membranes — Mitochondria have their own cell membranes, just like a prokaryotic cell does.

DNA — Each mitochondrion has its own circular DNA genome, like a bacteria's genome, but much smaller. This DNA is passed from a mitochondrion to its offspring and is separate from the "host" cell's genome in the nucleus.

bacteria/mitochondria structural comparison



Reproduction — Mitochondria multiply by pinching in half — the same process used by bacteria. Every new mitochondrion must be produced from a parent mitochondrion in this way; if a cell's mitochondria are removed, it can't build new ones from scratch.

bacteria/mitochondria reproduction



Then we were required to do the SCL activity in group. We were given a task to complete the Venn diagram to compare and contrast of chloroplasts and mitochondria.



After that, we had learned about the division cycle of plant cell and totipotency. At the end of this lecture I will able to describe different stages of cell cycle and what is entails, apply cell cycle to plant growth and development, define totipotency and explain types of totipotent cells in plants and lastly can relate the control mechanisms involved in cell cycle with plant totipotency.

Eukaryotic cell cycle consists of : 1) GAP 1 (G1) phase-growth and doubling of cell organelles

2) Synthesis (S) phase- DNA replication occurs

3) GAP 2 (G2) phase-Preparation for cell division

4) M phase-division of the nucleus and cell



Eukaryotic cell cycle



Plant cell cycle-Mitosis





The passage of a cell through the cell cycle is controlled by proteins in the cytoplasm which is Cyclins.

· a G1 cyclins (D cyclins)

· S-phase cyclins (cyclin A)

· Mitotic cyclins (B cyclins)

· Their leves in the cell rise and fall with the stages of the cell cycle





The regulation of cell cycle



Plant growth can be by increasing cell numbers or increasing cell size. Body complexity is another dimension of plant growth. Plant have open growth strategy-continously produce new organs throughout their life due to the presence of a tissue called meristematic tissue. Meristematic tissue can be found in the following locations :

· Near tips of roots and stems called apical meristems

· In the buds and nodes of stems – axillary meristems

· In the cambium between the xylem and phloem in dicotyledonous trees and shrubs

· Under the epidermis of dicotyledonous trees and shrubs (cork cambium)

· In the pericycle of roots, producing branch roots/lateral roots.




Meristematic tissue




Next, we had learned about totipotency. What is totipotency? Totipotency is the ability of a single cell to divide and produce all of the differentiated cells in an organism. Spores and Zygotes are examples of totipotent cells. In the spectrum of cell potency, totipotency represents the cell with the greatest differentiation potential. Loss of totipotency is probably due to the genetic or epigenetic. Callus is made up of a group of unorganized loose parenchyma cells which proliferate from parent cells

.
Finally we learned about the factors that affect cellular totipotency. The factors that affect cellular totipotency are source of explant, nutrient media and constituents and culture environment. I love this topic because I had learned the new things in my life. I had never knew about totipotency before.

Discocery of cells

In week 4, we had learned about discovery of cells. At the end of this lect

ure, we will able to explain the cell theory and its implication, describe the characteristics of living things, compare and contrast a prokaryotic and eukaryotic cells and virus characteristics and lastly determine whether a cell is prokaryotic or eukaryotic or virus based on description given.

We are given a task to find out the name of scientist based on contribution to cell theory, date of discovery and illustration of their discovery or invention. For the first scientist was Robert Hooke (1665). He was discovered cell while looking through a slices cork and he also described cells as tiny boxes or honey comb. He thought cells only existed in plants and fungi. His invention was microscope.



Robert Hooke (1665)



For the next scientists was Anton Van Leeuwenhoek (1673). He used his hand made microscope to view samples from a pond and discovered single cell organisms. He improved magnification by polishing lenses and discovered bacteria from a sample of saliva from his mouth.



Anton Van Leeuwenhoek (1673)



Next for Theodore Schwann (1839) was discovered that animals were made up of cells. His invention was published micrograph that declared all animals and plants are made from one single fundamental unit.



Theodore Schwann (1839)




Lastly, Rudolf Virchow (1855) stated that all living things come from other living things. His invention was published a scientific journal about cell that form from division and support Schwann’s and Schleiden’s explanation about the origin of cells.



Rudolf Virchow (1855)



Other than that, we have find out the cell theory. According to what I had learned about cell theory during my matriculation session was all living things are made up of cells, cells are the basic units of structure and function in living things and living cells come only from other living cells. For the modern cell theory has additional 4 statements which were the cell contains hereditary information which is passed on from cell to cell during cell division, all cells are basically the same in chemical composition and metabolic activities, all basic chemical and physiological functions are carried out inside the cells (movement, digestion, homeostasis etc) and cell activities depends on the activites of subcellular structures within the cell (organelle, nucleus and plasma membrane).

Next, we have to find out the similarities and differences between prokaryote and eukaryote. The similarities are they both have DNA as their genetic material, they are both membrane bounded organelles, the both have ribosomes, the have similar basic metabolism, the are both amazingly diverse in forms.





Prokaryote vs eukaryote cells



The differences between prokaryotic and eukaryotic cells



Now, we were going to talk about archaea cell wall. Members of the domain Archaea cell walls composed of protein , a complex carbohydrate, or unique molecules resembling but not the same as peptidoglycan. Then I had learned about capsules/slime layers, bacterial cell membrane, nucleoid region, flagella and pili, endospores, plasmids, reproduction and metabolism. Moreover we also had knew the beneficial bacteria and pathogenic bacteria. Examples in using beneficial bacteria is remove pollutants from water, air and soil and for pathogenic bacteria can cause diseases such as E.coli.



Example on beneficial bacteria : Nitrogen fixation



Besides, we also had learned about viruses. At the end of this lecture, we will able to describe the structure and properties of a virus, compare a virus with a free-living cell and describe what viroids and prions. I had learned about the properties of virus which were no membranes, cytoplasm, ribosomes, or other cellular components. Viruses also cannot move or grow and they can only reproduce inside a host cell etc.





Examples of virus

Viruses can be classified according to their genetic material, virus shape, symmetry of capsid, presence or absence of the envelope and type of the host. Viruses reproduce in 2 ways lytic cycle and lysogeny cycle.



Lytic cycle and Lysogeny cycle



Next, we move to prions. Prions is an infectious agent that is composed primarily of protein. It was propagate by transmitting a mis-folded protein state. The process is dependent on the presence of the polypeptide in the host diagram. Prions implicated in number of diseases in a variety of mammals. The specific protein that the prion was composed of is also known as the Prion Protein (PrP). (PrP) is found throughout the body, even in healthy people and animals. Example of prion diseases are Alzheimer’s and Parkinson’s dieseases.




The prion theory



Example of prions



Lastly for this week lecture, we had learned detail about Viroids. Viroids is a small circular RNA molecules wihout a protein coat. A viroid can contain as few as 250 nucleotides and viroids only infect plants. The viroid induced diseases lead to dramatic economy losses in agriculture and horticulture worldwide.




Viroids can cause severely misshaped potatoes





Then, we were given a task to do the flyers about the most wanted and the most unwanted bacteria. We were doing discussion in groups and decided to choose the most unwanted bacteria which was Pseudomonas aeruginosa. The aim to this activity is to expose the students to various beneficial and pathogenic Bacteria as well as to know the its economic importance. Next, we had required to watch the video about on history cell of life.

                             

The history of life

      In week 3, we learned about new topics which was about History of Life. I able to describe the conditions thought to have existed on early earth. How did life begin?? We never know how old our earth as well but for this topic I had learned about that diversification of life started in 3.8 billion years ago. How did life begin?? It was begin from molecule to cells. The first cells was from abiotic synthesis of small organic. Next, bonding small molecules into macromolecules. Then, packaging macromolecules into protobionts and lastly origin of self-replicating molecules.  

         Origins of life means organic life sprung from non-organic matter exclusively through a natural mechanistic process on a pre-biotic earth. This is called chemical evolution. That original life form then evolved into more complex life forms through a natural process of random mutations and natural selection.

         Origin of life in chemical evolution was from small inorganic molecules CO2, N2, H2, CO, NH3, H2S, H2O and then into small organic molecules. Next, into larger organic molecules which was RNA, DNA, proteins etc and then turn into life. It approximate 4.6 billion years ago earth formed. How did organic molecules formed on primitive earth? They could have formed from smaller molecules present on primitive Earth, either very slowly over millions of years or rapidly before the earth cooled down. Prebiotic broth hypothesis. Asteroids may have brought them from outer space. According prebiotic broth hypothesis which was proposes that organic molecules formed near earth’s surface-in a sea of organic soup or on rock or clay surfaces.

        Furthermore, we also had being explained about Miller-Urey’s experiment (1953). It was established an experimental reducing atmosphere. The mixture was subjected to electrical sparks and cooled the systems. The simple organic compound reacted in water to form amino acids. I had never heard this before so for me it was quite interesting that I had learned in the class. 

                                              

                                           

                                                                  Miller-Urey’s experiment

Next, I had learned about the RNA world. We always get confused on which came first? RNA or DNA? So in this subtopic I knew that the first genetic material was probably RNA, not DNA. DNA strands can only copy themselves with the help of enzymes but single RNA strands can copy in solutions containing nucleotides without enzymes. This theory is called the RNA world theory. 

                                                      

                                                     The structures between DNA and RNA

Moreover, we had learned about protobionts. Protobionts were from replication and metabolism and then aggregates of abiotically produced molecules enclosed by a membrane. Next display simple replication and metabolism and also maintain an internal chemical environment.

                      In this class, we knew the first prokaryotes. It could be chemoheterotrophs-consume organic molecules for both energy and carbon. “ate” ATP energy formed abiotically in the organic soup. The loss of abiotically formed ATP, natural selection will favour those early prokaryotes that can regenerate ATP from ADP using energy extracted from available compound.

                   So for the origin of life by 2-2.5 billion years ago, there was a great diversity of prokaryotes on earth which were firstly is anaerobic heterotrophs and autotrophs and secondly aerobic heterotrophs and autotrophs. Starting from when life began, until 2.1 billion years ago, all life was prokaryotic, unicellular and aquatic!

                   For the SCL activity, we are required to do the comic strips which were quite interesting. We had to do the comic strips about evolution. For our group members, we had chosen tortoise for the main character in our comic strips. It was about a natural selection between saddleback tortoise and domed tortoise. Our group was doing together for finished the task and submit it into the putrablast website.

                                                         Natural selection for tortoises 

                     For the next subtopic we had learned about systematics, taxonomy and classification. At the end of this lecture, we will able to justify the use of scientific names and classification of organisms, arrange the Linnaean categories in hierarchical fashion, apply the concept of shared derived characteristics to the classification of organisms and lastly able to describe the present methods of molecular biology used by taxonomists.

                      All living things are classified by characteristics into 6 kingdoms of life which were archaebacteria, eubacteria, Protista, fungi, animals and plants. I had learned this topic which was biodiversity during my matriculation. So it will be much easier for me to understand for this particular topics. Biodiversity is very interesting because we can know all about living things.

                                              

                                                                         6 kingdoms of life

                  What is systematics? Systematics is the study of biological diversity and its evolution. Taxonomy, a subdivision of systematics, is the science of biological classification-identification, nomenclature ( naming the organism ) and making into a system.

                                                

                                                       Systematics, taxonomy and classification

       Classifications is the systems that help to clarify relationships among organisms; they help us remember organisms and their traits; they unable us to communicate clearly the identity of organisms being studied; they improve our predictive powers and they provide.

       Caralus Linnaeus was the first to develop and publish the first comprehensive and consistent classification system for both plants and animals. I also learned on how to naming the organism for example Homo sapien, Escheria coli. Genus is always capitalized, species is usually not. Both names must be underlined or written in italics. Species were arranged in an ascending series of inclusive categories of taxa.

                                           

                                                             Linnaeus classification categories

           Lastly, we had learned about phylogenetics. Phylogenetics is the study of evolutionary relationships among and between species. Homology means similar structure and position but different function-derived from a common ancestor. Analogy means similar function but different origin which was not derived from a common ancestor; convergent evolution-similar selection pressure.