SCIENCE NOTES PDF

SCIENCE NOTES ​ Scientific Method and Biological Nomenclature​ A review on the fundamental skills in biology​ ​ First name: Species name​ Second name: Specific Epithet​ ​ Rules for Writing Scientific Names:​ ​ 1. Use Binomial Nomenclature: scientific names consists of two parts, the Genus name (capi...

SCIENCE NOTES ​ Scientific Method and Biological Nomenclature​ A review on the fundamental skills in biology​ ​ First name: Species name​ Second name: Specific Epithet​ ​ Rules for Writing Scientific Names:​ ​ 1. Use Binomial Nomenclature: scientific names consists of two parts, the Genus name (capitalized) and the species name (lowercase)​ ​ Example: Homo sapiens​ ​ Homo = genus​ sapiens = species name/specific epithet​ ​ 2. Italicize or Underline​ ​ Example: Homo sapiens​ ​ 3. Language: Scientific names are generally in latin or in Latinized forms.​ Why latin? : Because it’s a dead language, so it will never change. ​ 4. Abbreviating Genus Name: After the first mention, the genus name can be abbreviated to its initial, followed by the full species name.​ ​ Example: Escherichia coli becomes E. coli. ​ 5. Subspecies: When mentioning subspecies, include a third name​ ​ Example: Homo sapiens sapiens​ ​ Why do scientists get fancy with scientific names? - Universal language - Avoids confusion - Precise Identification - Shows relationships​ Introduction to biology BIOLOGY is an inquiry about life Attributes Order Composed of cells reproduction Evolution Energy processing Growth and development Response to Stimuli Homeostasis Natures Blueprint​ BIOMIMICRY Innovations inspired by life​ Biomimicry​ greek words: bios (life) and mimesis (limitation)​ practice of learning from and mimicking nature's designs processes, and systems to solve human challenges and create sustainable innovations ​ Japanese bullet train from kingfishers beak​ Engineers redesigned the train's nose to mimic the streamlined break of a kingfisher which allows it to dive into water with minimal splash. This reduced air resistance noise and energy consumption.​ ​ Wind Turbine Blades from fins of humpback whales​ engineers used the tubercles (bumps) on whale fins to design turbine blades that improve energy efficiency by reducing drag and increasing lift.​ ​ Investigation Station​ In 1991 an architect from Zimbabwe was hired to design the largest retail and office building in the country. However the building's owner did not want to pay for the high cost of air conditioning. What natural innovation do you think inspired him to design a self cooling building?​ Biomimicry proves the fact that nature and man’s technology can co-exist The Cellular level of organization​ What is the smallest living organism?​ ​ Smallest living organism​ Mycoplasma genitalium = Unicellular (ONE CELL)​ M/ genitalium, a parasitic bacterium which lives in the primate bladder, waste disposal organs, genital, and respiratory tracts, is thought to be the smallest known organism capable of independent growth and reproduction. With a size of approximately 200 to 300 nm.​ ​ What is the largest living organism​ ​ Armillaria solidifies (HONEY FUNGUS) = Multicellular (MULTIPLE CELLS)​ A network of this fungus in the pacific northwest spans 5.5 kilometers across, covering about 2384 acres. It is estimated to be over 2000 years old.​ SW COVERAGE BELOW​ Cell Cycle​ ​ The cell cycle represents a self regulated sequence of events that controls cell growth and cell division. The goal of the cell cycle is to produce two daughter cells. Each containing chromosomes identical to those of the parent cell.​ ​ 1 cycle for a human takes = 24hrs​ ​ GO → gap zero​ → reaching stage​ ​ Example of a Complex Cell: Brain cells​ 2 Phases: Mitosis & Interphase​ ​ 5 phases: prophase, metaphase, anaphase and telophase, and cytokinesis.​ ​ Meiosis → sex cells​ → male = sperm cell​ → female = egg​ ​ A. interphase: It represents continuous growth of the cell and is subdivided into three phases​ G1 |gap 1| phase. Phase S (synthesis) phase​ G2 |gap 2| phase.​ ​ B. Mitosis ​ Karukyonesis - nucleus​ Cytokinesis - cytoplasm​ ​ ​ G1 Phase​ - usually the longest and most variable phase of the cell cycle​ - begins at the end of M phase​ - cell gathers nutrients and synthesizes RNA and proteins necessary for DNA synthesis and chromosome replication​ ​ - it has to ensure the cell is ready to replicate the DNA​ → there should be cell growth ​ → amino acids​ → DNA is a protein, so they should collect amino acid (energy reserves)​ → nucleotide​ ​ S Phase​ - Initiation of DNA synthesis ​ - DNA is doubled (because: produce two identical sets of chromosomes.)​ - formation of new chromatids.​ ​ G2 Phase ​ - cell continues to grow and protein synthesis continues in preparation for mitosis​ Further cell growth. ○​ Production of microtubules and other proteins essential for mitosis. ○​ Final checks to ensure DNA replication is complete and error-free. ○​ G2 Checkpoint: Ensures all DNA is replicated and repairs any DNA damage.​ ​ 1.)​ Ribosomes - protein 2.)​ Mitochondria - energy​ ​ These organelles are present in the G2 Phase​ ​ MITOSIS (M) PHASE​ ​ Mitosis is a process of chromosome segregation and nuclear division (karyokinesis) followed by cell division(cytokinesis) that produces two daughter cells with the same chromosome number and DNA content as the parent cell. ​ a. Prophase ​ Chromatin condenses into visible chromosomes.  ​ Nuclear envelope begins to break down. ​ The spindle apparatus starts to form, originating from centrosomes that migrate to opposite poles. b. Prometaphase (included in metaphase) ​ Nuclear envelope fragments completely. ​ Spindle fibers attach to chromosomes at their kinetochores (protein structures on centromeres). c. Metaphase ​ Chromosomes align at the metaphase plate (the cell's equatorial plane). ​ Metaphase Checkpoint: Ensures that all chromosomes are correctly attached to the spindle apparatus and aligned. d. Anaphase ​ Sister chromatids are separated as spindle fibers pull them toward opposite poles of the cell. ​ Chromatids are now referred to as individual chromosomes. e. Telophase ​ Chromosomes reach opposite poles and decondense back into chromatin. ​ Nuclear envelopes reform around each set of chromosomes, resulting in two nuclei. 3. Cytokinesis: Division of the Cytoplasm Cytokinesis is the final step of the cell cycle, involving the physical separation of the cytoplasm to form two daughter cells. a. In Animal Cells ​ A cleavage furrow forms, driven by a contractile ring of actin and myosin filaments, which pinches the cell into two. b. In Plant Cells  ​ A cell plate forms along the center of the cell, eventually developing into a new cell wall that separates the daughter cells.​ THE CELL CHECKPOINT ​ Apoptosis ​ ​ Cell Cycle Checkpoints​ - one of the several points in the eukaryotic cell cycle at which the progression of a cell to the next stage in the cycle can be halted until conditions are favorable​ - to prevent a compromised cell from continuing to divide​ ​ the fate of the cell can fix til conditions are favorable, but apoptosis (death) can happen​ ​ THE G1 Checkpoint​ - determines whether all conditions are favorable for cell division to proceed​ - growth factors, play a large role in carrying the cell past the G1 checkpoint​ - check for genomic DNA Damage ​ - a cell that does not meet all the requirements will not be allowed to progress into the S phase​ ​ - parent DNA​ - cell size​ - protein reserves​ ​ THE G2 CHECKPOINT​ - Ensure that all of the chromosomes have been replicated and that the replicated DNA is not damaged.​ - If the checkpoint mechanisms detect problems with the DNA, the cell cycle is halted and the cell attempts to either complete the DNA replication or repair the damaged DNA.​ ​ THE M CHECKPOINT​ - occurs near the end of the metaphase stage​ - also known as the spindle checkpoint​ - determines whether all the sister chromatids are correctly attached to the spindle microtubules​ - cycle will not proceed until the kinetochores of each pair of sister chromatids are firmly anchored to at least two spindle fibers.​ ​ Chromosome: Condensed DNA​ ​ ​ REGULATOR MOLECULES OF THE CELL CYCLE​ - Two groups of intracellular molecules that regulate the cell cycle:​ 1. Promotes progress (positive regulation)​ 2. Halts the cycle (negative regulation)​ ​ POSITIVE REGULATION OF THE CELL CYCLE​ - cyclin and cyclin-dependent kinases (CDKs) are responsible for the progress of the cell​ - the levels of the four cyclin proteins fluctuate in a predictable pattern​ - cyclins degrade after the cell moves to the next stage of the cell cycle​ ​ CDKs are enzymes activated by cyclins that phosphorylate target proteins to drive the cell cycle forward.​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ CDKs and Cyclin pairings​ 1. D-type cyclins bind CDK4 CDK6​ 2. E-type cyclins bind CDK2​ 3. A-type cyclins bind CDK2 or Cell Division Control 2 (CDC2)​ 4. B-type cyclins bind CDC1​ ​ In Summary​ ​ G1 / S transition: Cyclin D activates CDK4/6 to progress the cell from G1 to S phase​ ​ S phase entry: Cyclin E CDK2 facilitates the initiation of DNA replication​ ​ G2/ M Transition: Cyclin B CDK 1 promotes mitotic entry.​ ​ Negative Regulation of the Cell Cycle​ - halt the cell cycle​ - Examples: p53 and Retinoblastoma protein (Rb) ​ ​ Role of p53 recruit enzymes that are responsible for repairing the DNA.​ If damage cannot be repaired, p53 activates apoptosis.​ Enzymes are recruited to try to fix the problem, but if it cannot be fixed, p53 activates apoptosis​ ​ Role of Rb​ Blocks the transcription and the production of proteins necessary for G1/S transition when the cell is small in size. ​ ​ - E2F is important for transcription​ - If there is not E2F, replication of DNA would not be possible​ - If the size is not enough, replication of DNA would not be possible​ ​ The Regulation of the cell​ Rb and other proteins that negatively regulate the cell cycle are sometimes called tumor suppressors. ​ ​ Cell Cycle Regulation and Cancer​ Cancer comprises many different diseases caused by a common mechanism: uncontrolled cell growth.​ ​ Proto-oncogenes​ - Genes that code for the positive cell cycle regulators​ Oncogenes - a mutated proto-oncogenes cause a cell to become cancerous​ Oncogenes differ from proto oncogenes in three basic ways​ 1. Timing and quality of expression​ 2. Structure of protein products​ 3. Degree to which their protein products are regulated by cellular signals. ​ ​ Chromosomal Aberrations​ - Structural or numerical changes in chromosomes that can lead to development anomalies, genetic disorders, or other physiological issues.​ ​ Structural aberrations​ - Structural changes occur when chromosomes are broken and incorrectly repaired, leading to alterations in their structure. ​ ​ 5 types of Chromosomal aberrations​ ​ ​ ​ 1. Deletion​ A part of the Chromosomes gets removed, a segment of a DNA or a section of chromosome is lost.​ ​ 2. Duplication​ A part of the Chromosome is duplicated and copied twice.​ ​ 3. Inversion​ Bases are reversed​ ​ 4. Insertion​ They insert a part of the parent chromosome to the new chromosome, was inserted into a non-homologous chromosome (a chromosome that is not paired with the original chromosome)​ ​ 5. Translocation​ There is a switching of bases between non homologous chromosomes.​ ​ Numerical Aberrations​ Numerical changes occur due to errors in chromosome number, often due to nondisjunction during meiosis.​ ​ 1. Aneuploidy​ - presence of an abnormal number of chromosomes​ ​ ​ ​ ​ ​ ​ ​ Polyploidy​ More than two complete set of chromosomes​ Usually done for Plants because it's beneficial for farmers. ​ ​ ​