Week 2-4 Biology: The Science of Life PDF

WEEK 2-4: Biology: The Science of Life August 2024 | Prepared by: Daniel Lance R. Nevado Biology (“bios” – Life; “logos” – study of) “study of life” Deals with structures, functions of living things, and their relationship with their environment. Characteristics shared by living...

WEEK 2-4: Biology: The Science of Life August 2024 | Prepared by: Daniel Lance R. Nevado Biology (“bios” – Life; “logos” – study of) “study of life” Deals with structures, functions of living things, and their relationship with their environment. Characteristics shared by living systems 1. Gathering and Using Energy 2. Maintaining Internal Balance 3. Responding, Adapting, and Evolving 4. Reproducing and Continuing Life 5. Living and Interacting 1. Gathering and Using Energy Cellular Respiration is a process by which energy is released by the breakdown of food substances. Energy is the ability of organisms to do work that allows them to move. Energy is produced when complex organic matter (biomolecules) are broken down into simple substances. Metabolism is the sum of all chemical processes and energy changes happening inside the body of an organism. 1. Gathering and Using Energy Nutrition is the process by which organisms acquire food in order to survive, grow, and reproduce. Mode of Nutrition and energy processing in several organisms Humans and animals derive energy indirectly Green plants obtain energy directly from Fungi obtain energy by absorbing from the sun by ingesting food. sunlight via photosynthesis nutrients from dead or living organisms 2. Maintaining Internal Balance Excretion is the process of removing waste. Metabolic waste products includes CO2, H2O, mineral salts, and nitrogenous waste products. Organs involve in the elimination is skin, lungs, liver, kidneys, large intestine, and urinary bladder 2. Maintaining Internal Balance Homeostasis is the maintenance of the body’s internal environment. In the organismal level, regulatory chemicals in the form of hormones control the functions of activities, growth, and development. Different organ systems help control the internal environment and maintain normal processes (heart rate, body temperature, and fluid environment of the cells) 3. Responding, Adapting, and Evolving Locomotion or Motility is the movement from one place to another. Corals are attached to a substrate after reaching adulthood compared to their juvenile stage. Plants also show slow movements of body parts like in flowers blooming, tendrils clinging for support, shoots bending toward light, and vines creeping as they grow Microorganisms also move from place to place using their locomotory organs such as cilia, flagella, or pseudopods. 3. Responding, Adapting, and Evolving Sensitivity or Irritability is the ability of an organism to respond appropriately to a stimulus. Tropism or response is the reaction of an organism to stimuli. Stimuli or external factors: light, sound, temperature, pressure, food sources, or presence of chemical substances. A Venus flytrap (Dionaea muscipula), a carnivorous plant, gets ready to snap close as an insect triggers its hair cells within 20 seconds of the first strike 3. Responding, Adapting, and Evolving Living things need to adapt because the environment where they live in varies and constantly changes. Individuals adaptation usually happens more slowly than responding to a stimulus because some changes need to occur in the organism. Athletes train in higher elevation for better endurance. The body will produce more red blood cells in response to lower oxygen level. 3. Responding, Adapting, and Evolving Evolution refers to the changes in the characteristics of a group of organisms (species) over time. Evolutionary adaptation Camouflage is the ability of some animals to change color and body structure in order to is a gradual or rapid blend with their environment. It is a way of adaptation to escape predators change in body structure or behavior to be better suited to survive in a new environment. Toucans have colorful beaks for eating insects or fruits and scaring predators away. Hummingbirds have pointed beaks to probe tube flowers for sweat nectar. 4. Reproducing and Continuing Life Development refers to the defined stages in the life cycle of a living thing from fertilization to death. Intussusception is a process where living things exhibit growth from within the cells. Growth is an increase in size and volume by converting food to become a part of body cells. Accretion which is a growth by external addition of substances for nonliving things. All living things undergo defined stages of development that all ends up in death. 4. Reproducing and Continuing Life Reproduction is a process by which genetic information is passed on from one generation to another as organisms produce offspring. DNA is used as a physical carrier of the transferred genetic information through sexual reproduction. Two types of reproduction: Sexual Reproduction is the union of sex cells from two parents produce a unique individual of their kind Asexual Reproduction occurs when an organism makes copies of itself. 5. Living and Interacting Living things exhibit a high degree of organization from molecular to cellular level. Life forms a hierarchy of organization from atoms to complex multicellular organisms. 5. Living and Interacting The immensity of the biological realm can also be views in a horizontal dimension to show the diversity and richness of organisms inhabiting the planet. Biologists classified organisms into three domains based on their similar characteristics The six kingdom of the living world divided into three domains of life Early Beliefs About the Origin of Life Spontaneous generation or Abiogenesis is the idea that life originates from nonliving matter. Proposed by Aristotle in the 4th century - 17th century Biogenesis is the belief that life originates from preexisting life. Several experiments have been conducted to prove these contradicting beliefs to explain how life came about: 1. Redi’s Experiment 2. Needham’s Experiment 3. Spallanzani’s Experiment 4. Pasteur’s Experiment 1. Redi’s Experiment (Francesco Redi) In 1668, the Italian physician Francesco Redi conducted an experiment that challenged the idea of spontaneous generation. Experimental setup involved rejecting spontaneous generation using maggots that arose from decaying meat. He concluded that life arose from living matter and not from spontaneous generation. 2. Needham’s Experiment (John Needham) In 1748, the English priest John Needham challenged Redi’s experiment. Needham’s experiment tested whether or not microorganisms can appear spontaneously after boiling. Needham concluded that life in the broth was caused by spontaneous generation, however, he did not heat it long enough to kill all the microbe in the broth. 3. Spallanzani’s Experiment (Lazzaro Spallanzani) In 1767, the Italian scientist Lazzaro Spallanzani, challenged Needham’s experiment. Uses two setup: both containers were boiled, but one setup was not sealed, allowing air to enter the flask. The results were not taken completely by the believers of abiogenesis. They claimed that Spallanzani excluded air from his sealed flasks, which they believed was needed for spontaneous generation to occur. 4. Pasteur’s Experiment (Louis Pasteur) It was only in 1861 through Louis Pasteur’s experiment that most scientists were convinced that spontaneous generation does not occur. Pasteur designed an experiment to test the idea that a vital element from air was necessary for life to occur. The experiment supported the theory of biogenesis and rejected spontaneous generation This evidence suggests that new organisms arise only when they are produced by existing organisms. Current beliefs about the Origin of Life Divine Creation Creationism is believed that life forms and everything in the universe were created through a supernatural power rather than naturalistic means. Spontaneous Origin Life evolved from inanimate matter. The famous Miller-Urey experiment suggested that lightning may have helped trigger the creation of the key building blocks of life. Panspermia Proposes that a meteor or cosmic dust may have carried to Earth significant amounts of organic molecules, which started the evolution. WEEK 2: Cell: The Basic Unit of Life August 2024 | Prepared by: Daniel Lance R. Nevado Cell Theory is the Unifying foundation Through his crude of cell Biology microscope, Leeuwenhoek discovered The cell theory was proposed to explain living creatures in the pond water, which he the observation that all organisms are named, animalcules composed of cells All organisms are composed of one or more cells, and the life processes of metabolism and heredity occur within the cells. Cells are the smallest living things, the basic units of organization of all organisms. The works of Schleiden and Schwann supported the idea that both plants and animals are composed of cells. Cells arise only by division of a previously existing cell. “Omni cellula e cellula” Prokaryotic Cells Prokaryotes are the simplest organism. Bacterial Structure: In bacteria, the cytoplasm is surrounded by a plasma membrane Most bacteria possess a cell wall, and sometimes also a capsule. The cell wall maintains the shape of the cell. This cell wall is composed of peptidoglycan, which consists of a carbohydrate matrix (polymers of sugars) that is cross-linked by short polypeptide units. Prokaryotic Cells Prokaryotes are the simplest organism. Bacterial Structure: In bacteria, the DNA is located in a single circular, coiled chromosome that resides in a region of the cell called the nucleoid. The many proteins specified by bacterial DNA are synthesized on tiny structures called ribosomes. Prokaryotic Cells Prokaryotes are the simplest organism. Bacterial Structure: Flagella (singular, flagellum) are long, threadlike structures protruding from the surface of a cell that are used in locomotion. Eukaryotic Cells Eukaryotic cells are far more complex than prokaryotic cells. The hallmark of the eukaryotic cell is compartmentalization. This is achieved through a combination of an extensive endomembrane system that weaves through the cell interior and by numerous organelles. The Nucleus Act as the Information Center The largest and most easily seen organelle within a eukaryotic cell is the nucleus (Latin, “kernel” or “nut”), first described by the Scottish botanist Robert Brown in 1831. Nuclei are roughly spherical in shape, and in animal cells, they are typically located in the central region of the cell. Many nuclei exhibit a dark-staining zone called the nucleolus, which is a region where intensive synthesis of ribosomal RNA is taking place. Chromatin: DNA packaging In eukaryotes, the DNA is divided into multiple linear chromosomes, which are organized with proteins into a complex structure called chromatin. When cells divide, the chromatin must be further compacted into a more highly condensed state that forms the X-shaped chromosomes visible in the light microscope. The nucleolus: Ribosomal subunit manufacturing These ribosomal assembly areas are easily visible within the nucleus as one or more dark- staining regions called nucleoli (singular, nucleolus) Ribosomes are the cell’s protein synthesis machinery Ribosomes are among the most complex molecular assemblies found in cells. Each ribosome is composed of two subunits (large and small subunit), each of which is composed of a combination of RNA called ribosomal RNA (rRNA). Ribosomes can be thought of as “universal organelles” because they are found in all cell types from all three domains of life. The Endomembrane System The interior of a eukaryotic cell is packed with membranes that form an elaborate internal, or endomembrane system. The presence of these membranes in eukaryotic cells marks one of the fundamental distinctions between eukaryotes and prokaryotes. The largest of the internal membranes is called the endoplasmic reticulum (ER). The rough ER is a site of protein synthesis The rough endoplasmic reticulum (RER) gets its name from its pebbly surface appearance. It appears to be composed primarily of flattened sacs, the surfaces of which are bumpy with ribosomes. The proteins synthesized on the surface of the RER are destined to be exported from the cell, sent to lysosomes or vacuoles (described later in this section), or embedded in the plasma membrane. The smooth ER has multiple roles Regions of the ER with relatively few bound ribosomes are referred to as smooth ER (SER). Enzymes anchored within the ER are involved in the synthesis of a variety of carbohydrates and lipids. An important function of the SER is to store intracellular Ca2+. In muscle cells, for example, Ca2+ is used to trigger muscle contraction. Another role of the SER is the modification of foreign substances to make them less toxic. In the liver, the enzymes of the SER carry out this detoxification. The Golgi apparatus sorts and packages proteins Flattened stacks of membranes form a complex called the Golgi body, or Golgi apparatus The individual stacks of membrane are called cisternae (Latin, “collecting vessels”), and they vary in number within the Golgi body. The Golgi apparatus functions in the collection, packaging, and distribution of molecules synthesized at one location and used at another within the cell or even outside of it. A Golgi body has a front and a back, with distinctly different membrane compositions at these opposite ends. The Golgi apparatus sorts and packages proteins Protein transport through the endomembrane system: Proteins synthesized by ribosomes on the RER are translocated into the internal compartment of the ER. These proteins may be used at a distant location within the cell or secreted from the cell. They are transported within vesicles that bud off the RER. These transport vesicles travel to the cis face of the Golgi apparatus. There they can be modified and packaged into vesicles that bud off the trans face of the Golgi apparatus Vesicles leaving the trans face transport proteins to other locations in the cell, or fuse with the plasma membrane, releasing their contents to the extracellular environment. Lysosomes contain digestive enzymes Membrane-bounded digestive vesicles, called lysosomes, are also components of the endomembrane system. They contain high levels of degrading enzymes, which catalyze the rapid breakdown of proteins, nucleic acids, lipids, and carbohydrates. Throughout the lives of eukaryotic cells, lysosomal enzymes break down old organelles and recycle their component molecules. Peroxisomes: Peroxide utilization Peroxisome contains enzymes involved in the oxidation of fatty acids. Peroxisomes get their name from the hydrogen peroxide produced as a by-product of the activities of oxidative enzymes. Peroxisomes also contain the enzyme catalase, which breaks down hydrogen peroxide into its harmless constituents—water and oxygen. Plants use vacuoles for storage and water balance Plant cells have specialized membrane- bounded structures called vacuoles. Vacuole actually means blank space, referring to its appearance in the light microscope. The membrane surrounding this vacuole is called the tonoplast because it contains channels for water that are used to help the cell maintain its tonicity, or osmotic balance. Mitochondria metabolize sugar to generate ATP Mitochondria (singular, mitochondrion) are typically tubular or sausage-shaped organelles about the size of bacteria that are found in all types of eukaryotic cells Mitochondria are bounded by two membranes: smooth outer membrane, inner folded membrane with numerous contiguous layers called cristae (singular, crista). The cristae partition the mitochondrion into two compartments: a matrix, lying inside the inner membrane; intermembrane space, lying between the two mitochondrial membranes. Chloroplasts use light to generate ATP and sugars Chloroplasts contain the photosynthetic pigment chlorophyll that gives most plants their green color. The chloroplast, like the mitochondrion, is surrounded by two membranes chloroplasts have closed compartments of stacked membranes called grana (singular, granum), which lie inside the inner membrane. each granum may contain from a few to several dozen disk-shaped structures called thylakoids. Surrounding the thylakoid is a fluid matrix called the stroma. chloroplasts, leucoplasts, and amyloplasts—are collectively called plastids. Three types of fibers compose the cytoskeleton Actin filaments are long fibers about 7 nm in diameter. Each filament is composed of two protein chains loosely twined together like two strands of pearls (actin) Microtubules, the largest of the cytoskeletal elements, are hollow tubes about 25 nm in diameter, each composed of a ring of 13 protein protofilaments Intermediate filaments are the most durable element of the cytoskeleton in animal cells is a system of tough, fibrous protein molecules twined together in an overlapping arrangement  Centrosomes are microtubule-organizing centers Centrioles are barrel-shaped organelles found in the cells of animals and most protists. They occur in pairs, usually located at right angles to each other near the nuclear membranes. The region surrounding the pair in almost all animal cells is referred to as a centrosome. Flagella and Cilia aid movement As pairs of microtubules move past each other using arms composed of the motor protein dynein, the eukaryotic flagellum undulates, or waves up and down, rather than rotates. Cilia are short cellular projections that are often organized in rows. Plant Cell walls provide protection and support The cells of plants, fungi, and many types of protists have cell walls, which protect and support the cells. In plants, primary walls are laid down when the cell is still growing. Between the walls of adjacent cells a sticky substance, called the middle lamella, glues the cells together. Some plant cells produce strong secondary walls, which are deposited inside the primary walls of fully expanded cells. WEEK 2-4: Biology: The Science of Life August 2024 | Prepared by: Daniel Lance R. Nevado