Jewel Peter                                                                                                                              Page 1Biology Honors SeminarProfessor ScottJan 11 2018Biology Honors Research Paper The study of life, or biology is a process that has been going on for thousands of years. The interest sparked in humans about who we are and the world around us gave us the original explorers and the information we have today. The fundamentals of different biologists such as Charles Darwin for evolution, help us delve and explore to expand our human boundaries. Like many biologists, the ultimate aim of the paper is to address how the cell differentiated, how it works, the stages of life, and how it obtained genes. The cell is made up of different parts that serve as an organ for a body. These are parts are known as organelles. The cell wall is a rigid layer of material that surrounds the cell of plants and some other eukaryotes like fungi. Its major goal is to protect and support the cells. For example, it helps plants not burst their cell because there is a rigid wall to prevent this from happening unlike the most of the animalia kingdom. Cell wall can be made from chitin for fungi and a stringy substance known as cellulose in plants. The chloroplast is found in plants and photosynthetic algae. Light dependent photosynthesis relies on the capturing of sunlight for photosynthesis while light independent photosynthesis is the synthesis of the new light in creating glucose.The cell membrane is a selectively permeable membrane found in eukaryotic cells. The cell membrane allows diffusion, movement of items from a high concentration to a low concentration. The three types of transport are passive, active, and osmosis. Passive transport is when items are moving with the concentration gradient, from a high to low. Simple passive transport is when molecules can easily slide through the phospholipid bilayer to reach their destination, either in or out. They don’t require ATP either because they are moving with the concentration gradient. Molecules small and uncharged, as well as glucose, fatty acids, oxygen, carbon dioxide, and gases are some of the items that can get through using simple passive transport. Facilitated passive transport is the transport of molecules from high to a low concentration using channels and protein pumps. These molecules are usually larger and specification to go to a certain area thus need assistance. The second type of transport is active transport. During active transport, ATP is being used to move molecules against the concentration gradient, molecules are moving from a low to high concentration. Usually large and charged (ions) molecules need this. The only specialized pump where this happens is the ATP pump where the opposite diffusion happens. Lastly, since water is needed for body to function, it can use pumps known as aquaporins or just simply be permeable through the cell membrane using simple diffusion. The latter is known as osmosis.Osmosis is the movement of solvent molecules like water through a semipermeable membrane into an area of higher solute concentration like salt, to attain homeostasis with the use of osmotic pressure to attain an isotonic solution. The cytoplasm is the region between cell membrane and nucleus. It is a clear, thick, gel like fluid that is constantly moving to help with the cell’s different processes. The two major anaerobic respiration processes happen here.Glycolysis is the first form of respiration that happens in the cell, in the cytoplasm. Glycolysis is the process that converts glucose ,C?H??O?, into pyruvate, to make 2 ATP. It can be both aerobic and anaerobic resulting in around 2 ATP. Fermentation is an anaerobic form of respiration when only glucose is present. The products include gases, water, and acids but no ATP.. The mitochondria is also another major ATP energy generator of the cell. Two major respiration processes that happen there are the Krebs Cycle and the generation of energy through the Electron Transport Chain (ETC). The Krebs Cycle occurs in the matrix of the mitochondria and breaks down pyruvate into carbon dioxide while extracting reactions. In total, the Krebs Cycle makes about 1-2 ATP. The final stage of cellular respiration is the electron transport chain (ETC). The ETC is a series of molecules embedded in the mitochondrial membrane, it is the sole process that makes most of the ATP needed. It happens in the cristae of the mitochondria to convert leftover ADP from the Krebs Cycle to ATP. The electrons passes different molecules until finally react with oxygen and protons to form water. The result is  around 32-34 ATP, water and carbon dioxide.The vacuole is an eukaryotic membrane bound organelle that stores excess. is present in all plant and fungal cells and some protist, animal and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic molecules including enzymes in solution, though in certain cases they may contain solids which have been eaten. Vacuoles are formed by the fusion of multiple membrane vesicles and are effectively just larger forms of these. The organelle has no basic shape or size; its structure varies according to the needs of the cell.The nucleus holds the genetic key, known as DNA, short for deoxyribonucleic acid. DNA contains the code for an entire cell. The nucleus houses the DNA because conditions outside in the cytoplasm will destroy DNA; thus only different RNAs will leave the cell to carry out processes. DNA replication is the process by which DNA is copied to create two identical daughter pairs. The first step is that DNA unwinds and separates using helicases, a protein that aids in unwinding DNA; the hydrogen bonds are broken. The second step is replication. The  first step of replication is that the DNA splits into two strands making a Y-shaped formation known as the replication for replicated fork. A homologous half is neccessary inorder for the prongs of the fork to match and form a new pair of strands. One of the separated strands is called the leading strand, which is constantly used for DNA synthesis while the other strand is responsible for the leading strand synthesis. The third step is the binding of corresponding bases to match the split DNA to zip them up. After the replication reaches the end of the DNA strand, it terminates, leaving the DNA replicated. The nucleus and ribosomes are both present in a process known as protein synthesis. Protein synthesis is the process by which cells make the required proteins they need. Part one of the process is known as transcription and occurs in the nucleus. First DNA unwinds and unzips breaking hydrogen bonds in the process. Thymine is replaced with Uracil. Corresponding mRNA strand will bind to the two split strands of DNA. and lastly the mRNA will leave through the nucleus pores. Part two of the process is known as translation. It occurs in the ribosomes which are located outside the nucleus free-floating or attached to the RER(rough endoplasmic reticulum). The mRNA made from transcription goes into the ribosome who itself has rRNA (ribosomal RNA). tRNA(transfer RNA) comes and translates 3 RNA at a time leaving behind an amino acid for each triple. The amino acids then link with peptide bonds forming a polypeptide chain. Lastly, the chain folds into a protein with the help of the golgi apparatus and RER. A cell is a singular and functional unit of an organism. Different types of cells have different types of organelles to perform its life-sustaining processes. The two different types of cell that exist today are eukaryotic and prokaryotic cells. Prokaryotic cells are unicellular organisms that lack organelles or other membrane bound units. The four major organelles found in prokaryotic cells are the plasma membrane(gateway), cytoplasm(transport + respirate), ribosomes(protein synthesis), and genetic material (like DNA and RNA).  Eukaryotic cells, one the other hand, are unicellular or multicellular organisms that have mostly specialized membrane bound organelles. Examples of eukaryotic organelles would be the nucleus(a membrane bound sac that holds DNA which gives out the commands), the chloroplast (a plant membrane bound organelle that holds chlorophyll for photosynthesis), the lysosome (an animal membrane bound organelle that breaks down excess and worn out organelles with digestive acid…mini stomach), the vacuole ( a membrane bound organelle that stores excess nutrients, water, and waste that did not leave the cell) and the mitochondria (a membrane-bound organelle that processes food into ATP energy). Similarities between eukaryotic and prokaryotic cells are that they have a chromosomes/DNA/RNA, plasma membrane, do process of cell division (either mitosis, meiosis, or binary fission) and do protein synthesis with the use of ribosomes. Differences between prokaryotic and eukaryotic cells are that prokaryotic organelles are much simpler than eukaryotic organelles. Prokaryotic organelles include the cytoplasm (for travel), ribosomes (for protein synthesis), and a cluster of dna centralized but lacking any sort of membrane. Eukaryotic cells contain multiple membrane bound organelles; the nucleus is a membrane that surrounds and protects DNA unlike prokaryotic plasmids, the mitochondria is a double membrane organelle that does cellular respiration, and the chloroplast is a membrane bound organelle for plants and plant-like protists that do photosynthesis with the chlorophyll inside. The endosymbiont theory, which stated that prokaryotes are other prokaryotes, and the autogenic theory, which stated that prokaryotic cells folded up and began to specialize in different cells, both prove the fact that prokaryotic cells evolved much earlier and is simpler than eukaryotic cells.The four major eukaryotic groups are plantae,animalia, fungi, and protista. Organisms in the animalia kingdom are multicellular and don’t have cell walls or photosynthetic pigments. All organisms in the animalia kingdom has some type of skeletal support and have specialized cells. In addition, these organisms have cellular, tissue, organ and system organization. All organisms in the animalia kingdom reproduce sexually instead of asexually.  All land plants such and water plants are found in the plantae kingdom. Organisms in the plantae kingdom produce energy through photosynthesis. In addition, organisms in the plantae kingdom have a cell wall and chlorophyll that catches light energy for photosynthesis, or synthesis of light to make glucose. The fungi kingdom is responsible for breaking down dead organic material and helps recycle nutrients through ecosystems. In addition, the majority of vascular plants(plants with xylem-phloem systems) rely on symbiotic fungi to grow. For plants,Symbiotic fungi are found in the roots of all vascular plants and provide them with important nutrients. For animals,Fungi provide many types of medications such as antibiotics and penicillin, but also cause many diseases. Fungal diseases are difficult to treat because fungi are similar to organisms in the animalia kingdom. Examples of fungal diseases include ringworm(A common fungal skin infection that often looks like a circular rash) and mucormycosis (A rare infection that mainly affects people with weakened immune systems). The last major kingdom of Eukaryotic domain are the protists. A protist is a eukaryotic organism that does not fit under the characteristics of animalia, plantae, or fungi. The protista kingdom includes unicellular organisms. Organisms in the protista kingdom need to live in an aquatic environment. The three types of organisms in the protista kingdom are protozoa, algae and fungus-like protists. Protozoa obtain their food with phagocytosis, which involves engulfing their prey with mouth-like structures. Algae contain chlorophyll and obtain their food through photosynthesis just like plants. Fungus-like protists absorb nutrients from their environment directly into their cytoplasm(phagocytsis). Slime molds are an example of fungus-like protists that commonly live in decayed wood. Malaria, a world-wide disease occurring in tropical climates, is caused by an animal-like protist known as  the Plasmodium. In the ocean, many plant-like protists live at the surface where they perform photosynthesis. There are major similarities and differences between the eukaryotic kingdoms. Animals, plants, and fungi are eukaryotic and mostly multicellular while protists are eukaryotic and unicellular. All except the animal kingdom can reproduce both sexually and asexually because they can only do sexual reproduction with the use of gametes. Plants can reproduce through asexual processes known as budding and fragmentation and sexually through by the use of gametes. Most fungi reproduce sexually by the use of gametes or asexually through fragmentation and budding. Lastly protists reproduce either sexually like animals and plants by the use of gametes or asexually through binary fission. Plants and plant-like protists are autotrophic (meaning they make their own food to use for energy) while animals, fungi, and animal-like protists are heterotrophic (meaning they consume food to use for energy). Plants contain cell wall made from cellulose, fungi contains cell wall made from chitin, and some plant-like protists may contain a cellulose-made cell wall.The two major subcategories of eukaryotic cells are the classification of its cells into somatic or non-somatic cells, also known as sex cells. Somatic cells are any cells in the body not used to reproduce. They contain 46 chromosomes or 23 pairs each in the human body being a diploid cell. Examples of somatic cells include bone marrow cells, blood cells, brain cells, intestinal cell etc. Sex cells, otherwise known as gametes or germ cells. Since it is used for reproduction, they are haploid. Being haploid means that you have 23 chromosomes each, thus it ensures that a human is made by giving it a total of the 46 chromosomes. Example of sex cells include the egg and sperm cells. Most somatic cells reproduce through a process called mitosis. Mitosis is a process of nuclear division in eukaryotic cells that occurs when a parent cell divides to produce two identical daughter diploid cells. During cell division, mitosis refers specifically to the separation of the duplicated genetic material carried in the nucleus. Meiosis on the other hand is a process that splits a cell into four daughter cells that are haploid, which means they contain half the number of chromosomes of the diploid parent cell. The kingdoms that have both somatic and sex cells are animals, plants, fungi because protists are just one cell and sexually reproduce through conjugation.Stem cells are unspecialized cells. The two types of stem cells are embryonic stem cells and adult stem cells. Embryonic stem cells are stem cells that have the capability of becoming anything they want to while adult stem cells only have the capability of being a certain type of cell. Embryonic stem cells are pluripotent meaning they can grow into whatever stem cell they want to be. The process of cell differentiation for the stem cell start when a signal to divide activates certain genes of proteins needed for the cell. The stem cell will then split; half into a specific cell (like blood cell) and the other half staying in the niche. The appearance of a certain gene (like the blood cell gene) on a cell is what gene expression is. Then the signals released transforms the split cell into a fully specialized cell (like the blood cell). As new signals signals pull through, it multiplies exponentially in the cell. To complete the transformation, most of the organelles and nucleus from the original stem cell is lost. The cell differentiation process is now finished and the new specialized cell will be sent to the area of need. This is the process by which a stem cell becomes a different cell, or the process of cell differentiation.The cell cycle is the cell division cycle taking place in the cell right before it is division/reproduction as well as the reproduction of each new cells using mitosis. The cell cycle is the period of time for a new cell to grow and do mitosis. After a cell is made, it directly enters the G1, or synthesis phase, phase, where rapid growth and metabolic is happening to develop the new cell—centrioles appear. The S phase, or synthesis phase, is where DNA replicate. Specific and accurate DNA replication is necessary to prevent genetic abnormalities which often lead to cell death and disease. G2 or the second growth phase mature the cell and organelles are doubled upon so it can enter the mitotic phase. In the M, or mitotic phase, the cell splits leaving behind 2 diploid cells from the original diploid cell. The M phase itself included telophase, that forms a new DNA membrane around the daughter cell and cytokinesis, which is the separation of the cytoplasm. After cytokinesis is finished, the process mitosis is done. Different genes control the rate (how slow or fast) cell reproduction happens. After the signal, the proto oncogene activates the cell cycle thus the  build up of cells happen over time. Too much of this can be a cause of the buildup of cells, or tumor. Thus another signal is sent to stop the buildup; with genes known as tumor suppressor. The balance of the cell cycle is maintained by equal signaling between both genes at different sites or the internal clock. The unbalance of these signals in forming cells is what causes cancer. Cancer involves an uncontrolled cell that develops into a tumor and spread throughout the body. Factors for this include chemical exposure, heredity with people who have cancer, radiation exposure, and UV rays which cause skin cancer. All of this can mutate either the proto onco or tumor suppressor gene that results in abnormal amounts of cell. The two types of cellular reproduction are mitosis and meiosis. Mitosis is an eukaryotic process that happens in its somatic cells. Mitosis is a form of asexual reproduction that creates identical parent-daughter diploid cells. The ultimate aim of it is simple: it is to create two diploid cells by separating chromatid. The first phase of mitosis is interphase where a diploid (2n) cell grows and gets ready for reproduction. Then in prophase the nuclear membrane dissolves and copied chromosomes pair up. In metaphase, chromosomes line up in the middle at the equator of the cell, known as the mitotic spindle. Afterward in anaphase, sister chromatids are pulled apart into chromosomes and a different nuclear membrane starts to form. Lastly,  in telophase the cell pinches in the middle and two new diploid (2n) cells are formed when the cytoplasm is pinched using the last process of mitosis known as cytokinesis. The second process of cellular production is known as meiosis. It is used for the process of creating sex cells. The process for creating 4 haploid gametes are part I: seperate the homologous pair and part II: separate chromatid. In Meiosis part I, interphase lets the cells grow to be able to reproduce. In the prophase stage, the chromosomes are visible due to the fact that the nuclear membrane has dissolved. Then the chromosomes line up together in metaphase forming a homologous pair. In anaphase, the homologous pair separates and goes to each side. In cytokinesis and telophase, the cell splits into two moving on of the chromosomes from the homologous pair to one side while the other on the other side. This stage of being is like the mitosis beginning and now we need to separate the chromatids. Since the cell already developed, interphase is skipped and jumps directly to prophase. In prophase II, the nuclear membrane once again is dissolved. In metaphase II, the chromatids line up in the middle. In anaphase II, sister chromatids are pulled apart chromosomes and a different nuclear membrane starts to form. Lastly,  in telophase the cell pinches in the middle and four new haploid (n) cells are formed when the cytoplasm is pinched using the last process of mitosis known as cytokinesis. Meiosis products contain half as many chromosomes in their cells than mitosis because the meiosis produces (egg cells and sperm cells) are then combined to form what is known as a zygote (the first fertilized egg containing all the chromosomes needed for growth). Meiosis unlike mitosis leads to variation traits in one of four ways. The first way is in the production of haploids. When making haploid cells, ½ of mom’s gene is added to ½ dad’s genes leading to a different combinations of genes. The second way is with the independent assortment that happens in metaphase I. During the lineup of middle for separation into different cells, the way they arrange when making the gametes help make a child more like one of their parents or equal. Crossing over in prophase I can happen with any genes, making the possibilities endless. Lastly nondisjunction, where one extra chromosomes go to one side, it can lead to different sex-linked/somatic disorders. Genes are made of DNA, in random assortment of patterns in bases A, T, C, G coding for all of the processes required for the body (like the process of making different proteins). As your cells develop and duplicate they pass on this genetic information to the new cells. Each time DNA splits and is duplicated, they pass a certain genetic code made possible by the regular DNA replication  or insertion, deletion, substitution, and frameshift. DNA is wrapped together to form structures called chromosomes. Most cells in the human body have 23 pairs of chromosomes, making a total of 46. Individual sperm and egg cells, however, have just 23 chromosomes (haploids). You received half of your chromosomes from your mother’s egg and the other half from your father’s sperm cell. A male child receives an X chromosome from his mother and a Y chromosome from his father; females get an X chromosome from each parent. Genes are sections or segments of DNA that are carried on the chromosomes determine specific human characteristics, such as height or hair color. Because you have a pair of each chromosome, you have two copies of every gene (except for some of the genes on the X and Y chromosomes in boys, because boys have only one of each). A mendelian gene is a gene that has a clear cut dominant vs recessive line. The genotype is either homozygous recessive in which recessive shows up and dominant isn’t present, heterozygous in which dominant shows up though recessive is present in gene, and lastly homozygous dominant in which dominant shows up and recessive isn’t present. An example of a mendelian trait in human cells are cheek dimples. Cheek dimples are dominant while no cheek dimples are recessive. (C- cheek dimples, c-no cheek dimples)-With heterozygous parents. (75% chance of cheek dimples and 25% chance of no cheek dimples).¼- homozygous dominant, ¼-homozygous recessive, 2/4- heterozygous… (1:2:1 ratio)-With homozygous recessive parents. (100% chance of no cheek dimples)4/4 homozygous recessive-With homozygous dominant parents ( 100% chance of cheek dimples)4/4 homozygous dominant-With two heterozygous dominant parents (100% chance  of cheek dimples )4/4 heterozygous When genes are not passed down correctly, it can have an effect on the protein/amino acid being made for doing a process or it can have no effect because the codon still codes for the same amino acid. The four types of mutations include insertion, deletion, substitution, and frameshift. Insertion is when extra base pairs are added changing the codon for the whole process of protein synthesis. Deletion is when base pairs are deleted/missing changing the codon for the whole process. Substitution is when one base pair is wrongly paired to another (example: CT, AG). Frameshift happens when multiple occurences of these mutation happen together to the same amino acid. Finally, is the processes of nondisjunction during meiosis and its effect on the zygote and developing baby. Nondisjunction during meiosis results in gametes with either too many or very few chromosomes. This in turn causes disorders known as down syndrome which is a result of an extra copy of chromosome 21, resulting in a wide range of physical and developmental delays.These are the answers to how the cell differentiated, how it works, the stages of life, and how it obtained genes. Biology, the study of life, has taken a little circle around the world on the major life processes and their effects on cells. The ever continuing process of biology is continually expanding the human mind to a whole new level.