Introduction to Cell and Molecular Biology PDF

NOTE HISTORY OF THE CELLS Theory of Pangenesis In order for an individual to produce sperm, Cells, and Structures they comprise, are too...

NOTE HISTORY OF THE CELLS Theory of Pangenesis In order for an individual to produce sperm, Cells, and Structures they comprise, are too the hand will produce sperm and will travel small to the male genitalia. Tenets - are clauses for a certain theory. A handful of pioneering scientists ad use their handmade microscopes to uncover a world that would never have been revealed to the naked eye. WHY IS THE CELL THE BASIC UNIT OF LIFE I.Robert Hooke (1665) - upon slices of cork. He observed that there are tiny/small chambers → This is because unlike other lower parts or lower within the cork. scope within your living organisms, they are unable The chambers looked like peas on cells to live outside the cell. He coined the term for cells with other scientists, Example: but he described the space he observed as “cell → If a scientist looks into a tissue, yung tissue natin like structures/cell referring to individual inmates pwede pa sila himayin into thinner cells. We can found in prison. observe fusiform cells II.Anton van Leeuwenhoek - animalcules → On a smaller scale, if we look into the nucleus, it He observed the fragments of animal liquids cannot replicate without the components found The theory of pangenesis was widely spread. within the cytoplasm. It means that in order for it to When we have animalcules, it means that the continue living, kailangan buo yung nucleus and liquid portion coming from the animal is a cytoplasm. Hence, the cell is the basic unit of life. miniature part of that animal. → When we say basic unit, hindi na siya pwedeng They observed that animalcules are different i-divide to remove, to maintain its function. So for looking under the microscope compared to what example, kapag tinanggalan si cell ng cytoplasm, they are. So yung mga cows , the liquid such as wala na siyang function na mag-digest or blood does not look like miniature cows na color mag-absorb ng nutrients, or mag-produce food. Pag red. natanggalan si cell ng nucleus, it is enucleated, wala He pioneered more ways in order to discover na siyang genetic material to pass down to the cells and how they behave in nature. succeeding cell likes. Example: The use of a swan neck bottle, that → Unlike the parts of a cell, which simply deteriorate causes spoilage of food. if isolated, whole cells can be isolated from III.Matthias Schleiden/Theodore Schwann - 2 tenets organisms and cultured in a laboratory where they of the Cell Theory will grow and reproduce for extended periods of a. All organisms are composed of one or more time. cells. → Yung cell natin kapag na-isolate given in a - One cell means they are unicellular certain environment, it is able to thrive. They can organisms. More cells are multicellular replicate just like microorganisms E.coli. They are such as humans and other animals. able to repopulate or create a colony given that their b. The cell is the structural unit of life environment is allowed to have ample nutrients for - All living organisms have cells, and these growth and allowed extended periods of time. cells are able to change or differentiate in → Death can also be considered one of the most order for it to specialize in a certain basic properties of life, because only living entities function. faces this prospect. IV.Rudolf Virchow - Third tenet of the cell theory → In order for an individual to die, it should first be c. Cells arise only by a division from pre-existing born. Magkakaroon tayo ng cell death because they cells. are alive. Why pre-existing cells? → The first culture of human cells obtained from a - In central dogma, during cell division malignant tumor from Henrietta Lacks was begun (genetics), one cell during mitosis by George and Martha Gey of Johns Hopkins produces 2 identical cells. That is why it is University in 1951. referred to as pre-existing cells, coming → In 1951 they discovered individual cultures' from your previous cells. hela line, cancer cell lines that are able to be used for cancer studies. → Even though Henrietta Lacks is already dead, her The more complex a structure: cell lines are still being used or sub-cultured for The greater the number of parts that must be future cancer studies. Siya yung first culture ng in their proper place; human cell. Siya yung pinaka-successful among The less tolerance of errors in the nature and thousands of isolates. First cell lines that can interactions of the parts; produce other cells aside from its own. And the more regulation or control that must → He took a malignant tumor and cultured it with a be exerted to maintain the system. growth media (it did not have cell death, rather it continued to multiply). When they subcultured the NOTE tumor , they observed that it was still growing. If you're going to look at the cell only, they are all → the culture of hela lines allowed multiple human able to produce certain materials. cell research in public and other researchers. It also helped us to understand the growth habit of tumor or Mitochondria and chloroplasts cell lines that has activated cancer genes. For breast - Specialized in production of ATPs cancer we have “brca 1 and brca 2). Nucleus - Specialized for the storage of genetic CELLS ARE HIGHLY COMPLEX AND materials ORGANIZED Vacuoles - In plants, they are able to store water in large → They are able to do various tasks. quantities to expand and for growth of the → When we say complex, their arrangement allows plants. them to perform specific task assigned to them - A more complex structure, meron siyang mas Example # 1: C4 plants maraming regulation and control to exert and → organization of different plants cells that allow maintain the system. them to convert light into a 4 carbon molecule Example for the cells itself instead of 3 for storage. - When you have extra chromosome 22, it is → it is important because it allows separate possible to have birth defects since may oxidation and respiration for plants and it is dagdag na genetic material. Also, kawalan ng becoming more popular and also more cost effective genetic material could cause malformation of in photosynthesis. Mas mataas yung yield nila as organelles in the body. Example XO females, compared to C3 plants. they can’t produce normal levels of hormones. →These type of samples, they have certain location Thus, iba yung kanilang regulation as or spacial separation, spongy mesophyll ng mga compared to normal individuals. halaman. One cell will provide oxidative photosynthesis while another cell will do the Organelles are found in areas that are strategic to respiration the other parts of photosynthesis. While maximize their efficiency. Also they are organized c3 plants does that depending on the time (morning in a sense that the location and the shape of each and night time) cells are specialized to whatever function they are going to do. Example #2 : Dermal cells → The dermis, epidermis and ‘yong mismong muscle tissue , they have different cell structures. CELLS POSSESS A GENETIC PROGRAM AND Although they have the same genetic materia, and THE MEANS TO USE IT genetic compositions. Those found within extremities specially found in dermis and epidermis, they have flattened cells and some of them are unti-unting Organisms are built according to information namamatay. As they go out of the body, nearing the encoded in a collection of genes, which are skin, mas maraming dead cells na makukuha. constructed of DNA. → Epidermis are not completely flattened cells. As you go outside or radially occurring yung cells, → Cells have their genetic programming. The unti-unting nagfflatten yung mga cells. genetic programming will lead to mRNA, tRNA, → Muscle cells, under epidermis and dermis, they rRNA, and later on the polypeptide proteins. These are “tapestrous” mukhang fusiform, tapered edges proteins will be expressed on certain mechanisms since they belong to the connective tissues. that allows for the production of the phenotype.  → The genetic code is different from one individual → they can also derive their energy from carbs in to another, unless they are kambal. They are able to plants or carbs that we can find in food. (i.e., we eat express those genetic materials. sinigang na baboy, we have protein and fibers). → Dito papasok yung concept ng dominant and Glucose is disassembled in such a way that its recessive alleles. energy content can be stored in a readily The less tolerance if errors in the nature and available form called ATP. interactions of parts; → when we eat glucose or starch, our body will And the more regulation or control that must catalyze it in order to produce ATP which we need be exerted to maintain the system. for movement and function of the body. Functions of → Meron tayong tinatawag na housekeeping genes, the body refers to the degradation of food to found in the cytoplasm that comes from the ovary or peroxisomes of the cells found in the lining of small the egg coming from the mother. and large intestines. →These genes are already present in cytoplasm that is signaling your embryo to differentiate (i.e., CELLS CARRY OUT A VARIETY OF CHEMICAL production muna ng spinal canal, then gastric canal, REACTIONS and the formation of head, tailbone, hanggang magkaroon ng limbs) they are controlled initially by →Cells both undergo catabolism and anabolism. maternal effect genes, and later on the genetic They are able to build certain compounds needed by makeup of cells itself. the body and are able to break down those specific compounds from food in order to utilize those substrates, so they have what we called enzymes. CELLS ARE CAPABLE OF PRODUCING MORE Cells function like miniaturized chemical power OF THEMSELVES plants. → this is just the cell division All chemical changes that take place in cells Reproduce by division, a process in require enzymes – molecules that greatly which the contents of a “mother” cell are increase the rate at which a chemical reaction distributed into two “daughter” cells occurs. The genetic material is faithfully → They are also able to fix broken materials, duplicated, and each daughter cell rejuvenation through catabolism and anabolism. receives a complete and equal share of → Kapag nagkaroon ng sugat yung open wound, genetic information. your platelets would produce thrombin. These → they are able to produce 2 daughter cells from 1 thrombin would increase and will stock and it will mother cell form mitosis. 4 daughter cells from cause cells to stock and stop the bleeding. As it is meiosis 2. stock there, ang mangyayari ay hindi na sila → they are duplicated because nagkakaroon tayo magcocontinue ng flow, however, kapag nag heal na ng duplication sa DNA through S-phase. yung sugat, they are going to degrade the thrombin → when we’re talking about meiosis, we have a wall with the stock RBCs and WBCs. reductional phase which is meiosis 1. →they have the capacity to fix and repair as long as there is a proper catabolism and anabolism. Because we have inborn errors of metabolism such CELLS ARE ABLE TO ACQUIRE AND UTILIZE as hemophilia (they are unable to produce normal ENERGY amount of clotting material, that’s why when they → In plants, we have P450, for photosystem 2 and have an open wound, matagal mag-heal since they a cone shape arrangement of chloroplast aside from can’t rapidly produce normal thrombin levels, and being stacking on thylakoids. even materials for reconstruction) kaya continuous → the cone shape material can harness light energy yung blood flow sa kanila. and convert it to chemical energy. The sum total of the chemical reactions in a cell Light energy is converted by represents that cell’s metabolism. photosynthesis into chemical energy that is stored in energy-rich CELLS ENGAGE IN MECHANICAL ACTIVITIES carbohydrates, such as sucrose or starch. For most animal cells, energy arrives → Some cells have motility or mobile function (e.g., prepackaged, often in the form of the sugar the WBCs in our immune system, as it flows in our glucose. bloodstream, they are very busy looking into the  gaps of each cell looking for possible viral exposed to water, kailangan tumaas yung surface infections or to which antibodies they are area interacting with water para mas mataas din attracted to). yung kapit or grip underwater. Cells are sites of bustling activity. Cells may respond to specific stimuli by altering Materials are transported from place to place, their metabolic activities, moving from one place structures are assembled and then rapidly to another, or even committing suicide. disassembled, and, in many cases, the entire → Example, facultative anaerobic bacteria are able cell moves itself from one site to another. to live with less oxygen, however they still need it at Initiated by changes in shape of “motor” certain cases (sometimes they prefer aerobic proteins. conditions para mas makapagproduce ng ATP → They also have structures that allow them to during aerobic respiration). destroy or build certain materials (e.g., our bone → Another example, sa plants since wala silang marrow continues to build our bones and other immune system, they have a programmed cell death skeletal structures; production of our motor instead. Kunwari may pumatong na harmful proteins or appendages that allow them to move, microorganism sa leaf ng plant, the plant then such as the flagella or cilia). signals the cells to kill itself. So while the microorganism is trying to reproduce in the adjacent cells, the plant counteracts by making sure the cells CELLS ARE ABLE TO RESPOND TO STIMULI adjacent to the affected cells are dead. Mapapansin A single-celled protist moves away from an ‘to sa “black spots” sa halaman where the object in its path or moves toward a source of programmed cell death occurred to contain certain nutrients. pathogenic materials. CELLS ARE CAPABLE OF SELF-REGULATION → In summary to the previous discussion, cells are able to create or do multiple things at once. For instance, they are able to do catabolism and anabolism at the same time, while also having cell replication. Each type of cellular activity requires a unique set of highly complex molecular tools (specially enzymes for the production of specific biomolecules needed by the cell for self regulation) and machines– the products of eons of natural selection and biological evolution. → For instance, kapag napunta na sa carbohydrate-depleted area, usually the cells would trigger na wala nang carbohydrate sa area so convert natin yung consumption sa body. For individuals, kapag wala na masyadong kinakain, our Macrophage phagocytosis cells convert to absorption ng ketones. → In the figure, macrophage is shown engulfing cells that are foreign to the body and later on tries to NOTE digest it. As they are being digested, their nutrients are absorbed by the cell and used for its Ketone is needed by the brain to function. Kaya metabolism. kapag sobrang gutom, aside sa sumasakit yung Most cells are covered with receptors that tyan, sumasakit din yung ulo caused by interact with substances in the environment in ketone-body absorption. highly specific ways. → Another example is yung pagkulubot ng kamay after ng matagal na pagbabad sa tubig. Recent CELLS EVOLVE studies show na it’s not due to osmosis, instead it is → In part of growing ng ating cells is also evolving. a reaction of the body in response to water. So once They are to change in order for it to survive. For the cells suitable to live, they have to adapt to their → Eukaryotes have divisions of cells into the environment. nucleus and cytoplasm, whereas prokaryotes have It is presumed that cells evolved from some nucleoid. Nucleoid is an area in which genetic type of peculiar life form non-living organic materials are concentrated. material that were present in the primordial → Although same sila ng ribosomes, prokaryotes seas. have 16 S and sometimes 18 S in eukaryotes. → We still have common housekeeping genes, i.e., → Complex membranous cytoplasmic organelles in for respiration and basic biochemistry of living eukaryotes such as golgi apparatus, endoplasmic organisms. However, we developed our specialized reticulum, nucleus. parts or appendages compared to our plant → Prokaryotes have no specialized organelles for counterpart. photosynthesis, however, they have plastids that are According to one of the tenets of modern able to harness light. They can still perform biology, all living organisms have evolved from photosynthesis without chlorophyll, thylakoid, and a single, common ancestral cell that lived grana. more than three billion years ago. → Eukaryotes in plants and animals have → There was a point in life where all living things are photosynthesis with chlorophyll. Photosynthesis is unicellular organisms. And looking in the past, all of no longer exclusive for plants, leaf sheep us started from one ancestor called LUCA. (Costasiella kuroshimae) is a sea slug that is able to Last universal common ancestor (LUCA). photosynthesize. → The genetic composition of our LUCA, they are → Eukaryotes have a cytoskeletal system, whereas mutatively identified as the collective of all living prokaryotes have none. However, they are still able organisms. If we are going to sequence all the DNAs to mobilize because of locomotory organelles such of living organisms, then identify all of the genetic as flagella and cilia. In eukaryotes, flagella and cilia material that are present to all, it is the remaining are found in unicellular eukaryotes only or in the genetic sequence of our LUCA. spermatozoa. →For nutrient derivation, prokaryotes can absorb nutrients directly from their environment, while EUKARYOTIC AND PROKARYOTIC CELL eukaryotes should implore phagocytosis (in phagocytosis, aside from eating the certain material, I. Differences: the stomach is going to break down the food and allow the small molecules of food to be absorbed by Eukaryotes Prokaryotes peroxisomes found in our cells for phagocytosis then use for metabolism) Division of cells into Nucleoid → Eukaryotes have cellulosic cell walls and can nucleus and cytoplasm sexuallly or asexually reproduce. In prokaryotes, they are only bound by asexual reproduction. 18 S ribosomes 16 S ribosomes I. Similarities: Complex membranous Plasma membrane of similar constitution cytoplasmic organelles Genetic information encoded in DNA using identical genetic code Specialized cytoplasmic No specialized ○ Although, sometimes prokaryotes have organelles organelles for differences in codon preference. Codon photosynthesis preference means a certain triad of genetic sequence may produce a different amino Cytoskeletal system acid for prokaryotes compared to its eukaryotic counterpart. Complex flagella and Simple compositions of Similar mechanisms for transcription and cilia locomotory organelles translation of genetic information (flagellin) Shared metabolic pathways Phagocytosis ○ Example: respiration, photosynthesis, glycolysis, glucolysis Cellulosic cell walls Peptidoglycan cell wall Similar apparatus for conservation of chemical energy as ATP Sexual reproduction Asexual reproduction ○ Most of it become ATP, NADPH, NADH Similar mechanism of photosynthesis  ○ For chlorophyllic prokaryotes and plants As a result of differentiation, different types of Similar mechanism for synthesizing and cells acquire a distinctive appearance and inserting membrane proteins contain unique materials. Proteasomes of similar constitution → Example, sa bone marrow, it contains a lot of calcium deposits, Ca2+, kaya it’s important to drink milk as you are trying to TYPES OF PROKARYOTIC CELLS grow to build your bone marrow. 1. Domain Archaea MODEL ORGANISMS Species that live in extremely inhospitable environments Cell and molecular biologists have focused They are often referred to as “extremophiles” considerable research activities on a small → They have specialized genetic number of “representative” models. functions (e.g., they can directly absorb Are organisms that are useful in representing a nitrites instead of carbohydrates for food. whole genera of other organisms. Methanogens (prokaryotes capable of ○ Characteristic: converting CO2 and H2 gasses into methane Their genetic composition (DNA) is (CH4) gas through metabolism) already sequenced. This allows changes in morphology to 2. Domain Bacteria be associated with certain genes. Includes the smallest known cells, the - Example: mycoplasma Plants: Arabidopsis thaliana Lacks cell walls A genome with fewer than 500 genes → Has few genes that are found in a small genome. Usually upon checking in online data resources such as NCBI, a whole genome of E. colli can be found that has less than 500 genes depending on the strain. Present in every conceivable habitat on Earth → Bacteria are also involved in humans, such as in our gut and skin microflora. TYPES OF EUKARYOTIC CELLS Arabidopsis thaliana In many regards, the most complex eukaryotic O If Arabidopsis induced a gene mutation in cells are not found inside of plants or animals, the tip called "patella," the flower petals but rather among the unicellular protists. disappear when they develop. This is → In unicellular protists, they are able to how they discovered new genes in produce all of the functions of the body with Arabidopsis. only one cell involved. For example, sea grapes is a unicellular organism pero may Microorganism: Yeast malaking appendages. ○ Yeast is faster to subculture An alternative pathway has led to the evolution ○ They are easy to mass produce of multicellular organisms in which different because they are microorganisms. activities are conducted by different types of specialized cells. → Differentiated cells are cells that change their physiological state in order to do a specialized function (i.e., motor cells, nerve cells). They have varying structures from our blood cells that are inoculated to produce a disk shape and create an increased surface area for the absorption of oxygen or removal of carbon dioxide. Yeast  o Escherichia coli Escherichia coli Mus musculus Worms: Caenorhabditis elegans Rabbit (Oryctolagus cuniculus) ○ For worms, C. elegans were ○ Used for cosmetics. commonly used. Zebrafish (Danio rerio) ○. ○ For neurofunctional studies, zebrafish are commonly used since they can regenerate even their brain stem when they are still young. How small is small? When we're talking about cell and molecular biology, we're going to look at how small that was to study. In CMB, we're looking at the cell and the molecular structure, as well as other components found within the cell. Two units of linear measure are most used to Caenorhabditis elegans describe structures within a cell: Insects: Fruit fly (Drosophila 1.) Micrometer (μm) melanogaster) One μm is equal to 10-6 meters. ○ For insects, D. melanogaster is Micrometer is equal to 103 nanometers. commonly used. It is widely used for 2.) Nanometer (nm) studying insects and development. One nm is equal to 10-9 meters. ○. One nm is equal to 10-9 meters. ○ Fruit flies have discs, and you can The angstrom (Å), which is equal to place the developmental disc from one-tenth of nm, is commonly their eyes onto their legs. Instead of employed by molecular biologists for legs, they will have six eyes at the atomic dimensions. location of their legs. This can be One angstrom is roughly equivalent to done during the development of the the diameter of a hydrogen atom. larvae. - Water o 4 Å in diameter DNA - 1nm and 2nm wide - To create a helix, it needs 10 Å. Cell - Chloroplast = 1 μm in diameter - Lymphocytes = 12 μm in diameter Drosophila melanogaster - Epithelial cells = 100 μm in diameter and 30 μm in height. Mammals: Mice (Mus musculus)  development of a virus inside the cell. 2. The translated protein coat will then engulf the viral nucleic acid until the cell bursts, releasing multiple viruses at once. All viruses are obligate intracellular parasites, meaning they require a host cell. ○ It is not necessarily true that when a human has HIV, it will develop into AIDS. Occur in a wide variety of very different shapes, sizes and construction but all of them share certain common properties. All viruses are obligate intracellular parasites; that is, they cannot reproduce unless present within a host cell. Depending on the specific virus, the host may be a plant, animal or bacterial cell. Outside of a living cell, the virus exists as a particle or virion which is a little more than a macromolecular package. ○ Virion – a virus without a host cell. ○ The macromolecular protein is a non-living organism; however, its survival depends on the virus. For instance, some viruses can survive longer on surfaces, such as the COVID-19 virus. B. VIROIDS An infectious agent consisting of a small circular RNA molecule that totally lacks a protein coat. ○ These cells are transported through the surfaces or connective orifices of the cell. ○ Cells can interact with different SPECIAL TOPICS environments through various cellular or protein pumps, which serve as passages Materials that are usually found within cell and for viroid movement. useful in molecular biology Theodor O. Diener coined the term viroid. The RNAs of viroids range in size from about A. VIRUSES 240 to 600 nucleotides, 1/10 the size of the Viruses can be protein coats or could also be smaller viruses. naked. ○ Since they are already RNA, they are ready Responsible for dozens of human diseases, for translation. When translation occurs, including AIDS (virus: HIV), polio, influenza, they will compete for mass production. cold sores, measles, and a few types of cancer. Very destructive to plants that are clonal. ○ They contain a protein coat and nucleic ○ Example: Banana acid which contain different types of DNA C. STEM CELLS allowing depth to be synthesized by the body or host. Stem cells are defined as undifferentiated cells 1. A virus will enter and attach itself to that: the host cell by injecting its nucleic 1. Are capable of self-renewal. That is, acid into the host cell to create a production of more cells like themselves. transcript, which is essential for 2. Are multipotent, that can differentiate into DNA/nucleic acid and the protein two or more mature cell types. coat. Since transcription occurs, Hematopoietic stem cells in the bone marrow translation follows, leading to the are an example of an adult stem cell.  ○ As we grow, our bodies become Are types of stem cells isolated (extracted) from differentiated. very young mammalian embryos. ○ However, inside our bones, they Unlike ES cells, the generation of iPS cells continuously produce young red blood does not require the use of an embryo. cells (nucleated RBCs). As nucleated This feature removes all the ethical RBCs are created, undifferentiated cells reservations that accompany work with ES cells can also be found. and makes it much easier to generate these ○ That's why stem cells are typically cells in the lab. obtained from human bone marrow. Undifferentiated iPS cells may give rise to teratomas. DIFFERENT TYPES OF STEM CELLS ○ Teratomas - are commonly benign; however, they can cause pain, and if they 1.) Embryonic Stem Cells (ES Cells) develop into malignant forms, they can cause cancer. Allows somatic cells and induces chemically, for it to revert into an undifferentiated cell which can be corrected using CRISPR technology or other genetic alteration. Its advantage was that since the cells are the same, the patient can easily accept them. However, its disadvantage is that since they are induced chemically, this can trigger the activation of cancer cells, leading to the production of teratomas. ENDOSYMBIOTIC THEORY ·States that eukaryotic cells came from were prokaryotic cells that can photosynthesize previously aerobic prokaryotes. 1. The nucleus from a nucleated embryo is ○ Mitochondria were once independent removed, leaving only the housekeeping cells, but they were absorbed and are genes active. 2. These housekeeping genes remain now used by eukaryotic cells. functional while the nucleus from a ○ Essentially, larger cells engulfed the somatic cell is inserted into the oocyte. smaller ones, and they became a part of 3. With the presence of maternal effect them. Since these smaller cells can genes in the oocyte, it can develop into produce their own energy, they provide a blastocyst. energy not only for themselves but also 4. The blastocyst is then cultured to for the larger cell. produce totipotent cells, which can differentiate into mature cells. ○ In return, the larger cell offers them ○ These cells are more likely to be protection and the nutrients needed for accepted by the patient when redelivers, growth. This is why mitochondria multiply as they share the same genetic along with the host cell during cell composition. division. ○ However, in some cases, rejection may occur if the blastocyst originated from a different patient. The egg would be allowed to develop to an early embryonic stage, and the ES cells would be removed, cultured and induced to differentiate into the type of cells needed by the patient. 2.) Induced Pluripotent Stem Cells