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This document contains Chapters 3 to 4 CHAPTER 3 CELLS AS UNITS OF LIFE CHAPTER OUTLINE 3.1. Cell Concept A. History 1. English scientist Robert Hooke described “little boxes or cells” in 1663 using a primitive compound microscope. 2. Dutch microscopist Anton van Leeuwenhoek made extensive observations and reported them in letters to Royal Society of London. 3. Advanced high-quality lenses in the early 19th century made it possible to examine cells. B. Cell Theory (Figure 3.1) 1. The cell theory asserts that all living organisms are composed of cells. 2. In 1838, Matthias Schleiden announced plant tissue was made of cells. 3. In 1839, Theodore Schwann concluded animals were made of cells. 4. In 1840, J. Purkinje described cell contents as protoplasm; modern understanding of cell organelles makes “cytoplasm” the preferred term. 5. In 1858, Rudolf Virchow, recognized that all cells came from pre-existing cells. C. How Cells Are Studied (Figure 3.2) 1. Light microscopes use light rays; they are limited in magnification and resolution. 2. The transmission electron microscope (TEM) uses electrons passing through the specimen. a. The wavelength of the electron is 0.00001 that of light, allowing greater magnification. b. Specimens must be prepared in thin section; the electrons pass through to a photographic plate. 3. Scanning electron microscope (SEM) scans electrons across a metal coated specimen; it has a lower magnification than TEM. 4. X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy may reveal the shape of molecules. 5. Cytology, the study of cells, has its own methods. a. Cells can be disrupted with most organelles in tact and centrifuged in a density gradient; organelles are then recovered. (Figure 3.3) b. Use of radioisotopes allows for tracing of metabolic pathways. c. Proteins are extracted and purified; antibodies prepared against the protein can be combined with fluorescent substances to detect the location of the protein. (Figure 3.13a) 3.2. Organization of Cells A. Prokaryotic and Eukaryotic Cells (Table 3.1) 1. Prokaryotes lack a membrane-bound nucleus found in eukaryotes. 2. However, both have DNA, use the same genetic code, synthesize proteins and use ATP. B. Components of Eukaryotic Cells and Their Functions (Figure 3.4) 1. The plasma membrane is the outermost membrane and regulates the entrance and exit of molecules. 2. A double membrane that separates the nucleus from cytoplasm encloses the nucleus. 3. Plant cells usually contain plastids for photosynthesis and have a cellulose-based cell wall. C. Plasma Membrane 1. The current model of membrane structure is the fluid mosaic model. (Figure 3.6) 2. The cell membrane is phospholipid bilayer in which protein molecules are partially or wholly embedded. 3. The phospholipid molecules have their water-soluble hydrophilic ends toward the outside and their fat-soluble hydrophobic portions toward the inside of the membrane. 4. The layer is liquid, providing flexibility; embedded cholesterols decrease this fluidity. 5. Glycoproteins are proteins with carbohydrates attached. (Figure 3.6) 6. Some proteins catalyze transport of substances such as ions across the membrane. 7. Others are receptors for specific molecules. D. Nucleus 1. Nuclear envelopes contain less cholesterol than cell membranes; pores allow relatively large molecules to readily move through. 2. Chromatin is a threadlike material that coils into chromosomes just before cell division occurs; it contains DNA, protein histones and nonhistone proteins. 3. Nucleoli are dark staining spherical bodies in nucleus and synthesize ribosomal RNA. 4. After transcription from DNA, ribosomal RNA joins proteins to form ribosomes. 5. Ribosomes are sites of polypeptide or protein synthesis. 6. Ribosomes are found free-floating in the cytoplasm or attached to the endoplasmic reticulum. 7. The outer membrane of nucleus is continuous with endoplasmic reticulum. E. Endoplasmic reticulum (Figures 3.7, 3.8) 1. The endoplasmic reticulum (ER) is a system of membrane channels continuous with outer membrane of the nuclear envelope. 2. The space between membranes of nuclear envelope communicates with channels (cisternae) in ER. 3. The rough ER is studded with ribosomes on cytoplasm side; products enter cisternae for transport to the Golgi complex. (Figures 3.9, 3.10) 4. The smooth ER functions to synthesize lipids and phospholipids. F. Lysosomes 1. Lysosomes are membrane bound vesicles produced by the Golgi complex. 2. Lysosomes contain digestive enzymes. 3. These enzymes help digest foreign material or engulfed bacteria: lysosome vesicles pour enzymes into a food vacuole or phagosome. (Figure 3.21) 4. They destroy injured or diseased cells; a healthy cell must maintain the membrane. G. Contractile vacuoles contain fluid and regulate ions and water. H. Mitochondria are present in nearly most eukaryotic cells. (Figure 3.11) 1. Mitochondria are bound by a double membrane; inner membrane folds (cristae) project into the inner space (matrix). 2. Enzymes on the cristae break down carbohydrate derived products; ATP production occurs here. 3. Mitochondria are self-replicating; their own DNA specifies some proteins; nuclear DNA codes other proteins. I. Cytoskeleton (Figures 3.12, 3.13) 1. The cytoskeleton is a network of filaments and tubules that maintain support and form. 2. In many cells, they provide cellular locomotion and movement of macromolecules and organelles. 3. The cytoskeleton is composed of microfilaments, microtubules and intermediate filaments. 4. Microfilaments are thin, linear structures first recognized in muscle cells. 5. Actin filaments are long, thin protein fibers that act with several dozen other proteins. 6. One of these is myosin; the interaction causes contraction in muscle and other cells. 7. Microtubules are composed of the protein tubulin (Figure 3.13); they move chromosomes during cell division. 8. Microtubules radiate out from a microtubule organizing center: a centrosome. 9. Centrosomes are not membrane bound. 10. Centrioles are short cylinders with 9 triplets of microtubules; centrosomes contain two centrioles lying at right angles to each other. (Figures 3.4, 3.14) 11. Intermediate filaments are larger than microfilaments and smaller than microtubules in size. 12. These filaments resist cell stretching and help to hold adjacent cells together. J. Surfaces of Cells and Their Specializations 1. Free surfaces of epithelial cells of tubes and cavities sometimes bear cilia or flagella. a. Single celled organisms may use cilia or flagella to propel forward. b. Flagella provide locomotion for male reproductive cells (sperm). c. Locomotory cilia and flagella both have a cylinder of nine pairs of microtubules encircling two single microtubules (9 + 2 pattern of microtubules). d. At the base of each cilium or flagellum is a basal body (kinetosome). 2. Ameboid movement uses pseudopodia. a. Ameboid movement is seen in embryonic cells, white blood cells and protozoa. b. Cytoplasmic streaming utilizes actin microfilaments to extend pseudopodia. c. Some specialized pseudopodia have cores of microtubules that assemble and dissemble. 3. Cell Junctions (Figure 3.15) a. In tight junctions, cell membrane proteins fuse to each other; they hold cells together so tightly that tissues (e.g., epithelial lining of stomach) form barriers. b. Adhesion junctions occur just beneath tight junctions; they encircle the cell but do not seal adjacent cells to each other. c. Desmosomes are “spot welds”; firmly attached to the cytoskeleton within each cell, are joined by intermediate filaments, and hold cells together with linker proteins to increase the strength of tissues in the heart, stomach and bladder. Hemidesmosomes are found at the base of cells and anchor them to underlying tissue layers. d. Gap junctions allow cells to communicate; tiny canals between cells allow the cytoplasm to be continuous in epithelial, nervous and muscle tissues. e. Some cell surfaces are plasma membranes which infold and interdigitate very much like a zipper zipper (e.g., epithelia of kidney tubules). 4. Microvilli are small finger-like projections of cell membranes such as those that line the intestine; also called brush borders, they increase absorptive area. (Figures 3.15) 3.3. Membrane Function A. Plasma Membrane; Dynamic and Selective 1. Also called the plasmalemma, it maintains cellular integrity. 2. It separates the interior environment from the exterior and regulates molecule traffic flow. 3. It provides many unique functional properties of specialized cells. 4. Internal membranes divide a cell into compartments; they are sites for most enzymatic reactions. B. Cell Membrane Function 1. The membrane is the gatekeeper to substances that enter and exit a cell. 2. Because the interior and exterior are different, the membrane is a critical controller. 3. Three principal methods are used for crossing a cell membrane: a. Diffusion along a concentration gradient, b. Substances bind to a site in a mediated transport system, and c. Endocytosis encloses a particle in a vesicle that is engulfed. C. Diffusion 1. Diffusion is movement of particles from higher to lower concentration, or along a concentration gradient. 2. If a membrane is permeable to a solute, diffusion will continue until concentrations are equal. 3. Most membranes are selectively permeable, only allowing some molecules to pass. 4. Most membranes allow free passage of water, gases, urea, and lipid-soluble solutes. 5. Water-soluble molecules (e.g., sugar), electrolytes and some macromolecules move across by carrier-mediated processes. D. Diffusion through Channels 1. Water and dissolved ions cannot pass through the phospholipid component of the plasma membrane. 2. Water and ions pass through the membrane by diffusion through pores created by transmembrane proteins. 3. Some channels are gated and require a signal to open or close them. 4. Gated ion channels may open or close in response to a signaling molecule (chemically-gated ion channels) or to the change of an ionic charge across the plasma membrane (voltage-gated ion channels). (Figure 3.16) 5. Water channels are called aquaporins. E. Osmosis 1. Osmosis is movement of water molecules down a concentration gradient across a membrane. (Figure 3.17) 2. Water flows across the plasma membrane via osmosis because the cytoplasm and surrounding external environment are often at differing concentrations. 3. Osmotic pressure is the pressure that resists the flow of water into the cytoplasm. 4. Marine fish have one-third the solute concentration as seawater; they are hyposmotic to seawater. 5. A marine fish swimming up a river delta would pass through a region where external and internal solutes were equal or isosmotic. 6. In freshwater, its blood solutes would be hyperosmotic to the freshwater. F. Carrier-Mediated Transport (Figure 3.18) 1. Special proteins (transporters or permeases) move nutrients and wastes across the membrane. 2. Permeases form a small passageway for very specific solute molecules. 3. When all transporters become saturated with solutes, the rate of influx does not increase with more solute; this measures the amount of transporter molecules. 4. With simple diffusion, the greater the difference in solute concentrations, the higher the flux. 5. Two mediated transport mechanisms are recognized. 6. Facilitated diffusion (or facilitated transport) permeases assist a molecule (e.g., sugar) to diffuse that otherwise cannot. 7. Active transport uses energy to transport molecules against the concentration gradient. (Figure 3.19) 8. Most animal cells require internal potassium levels 20–50 times outside levels; outside sodium levels may be ten times inside levels. 9. In many cells, sodium and potassium pumping are linked using the same transporter molecule. G. Endocytosis (Figure 3.20) 1. All processes (phagocytosis, potocytosis and receptor-mediated endocytosis) require energy. 2. Phagocytosis is common among protozoa and lower metazoa. a. An area of cell membrane coated internally with actin-and-myosin forms a pocket to engulf material. b. The membrane-enclosed vesicle detaches from the cell surface for internal digestion. 3. Pinocytosis a. Small areas of surface membrane invaginate into tiny vesicles called caveolae. b. Specific binding receptors for the molecule or ion are on this cell surface. c. It is involved in taking in some vitamins, hormones and growth factors. 4. Receptor-mediated endocytosis a. Plasma membrane proteins bind specific particles called ligands. b. This occurs in clathrin-coated pits coated with receptors. c. Brought within the cell, the pit is uncoated and the ligand disassociated to be recycled. d. Some proteins and peptide hormones are brought into cells by this method. H. Exocytosis 1. in this process, the membrane of a vesicle can fuse with the plasma membrane and extrude its contents to the surrounding medium. 2. This process allows for removal of indigestible residues, secretion of substances (such as hormones) and transportation of substances across a cellular barrier (transcytosis). 3.4. Mitosis and Cell Division A. Cell Types 1. All cells in nearly all multicellular organisms originated from division of a single cell, the zygote. 2. A zygote is formed from union of egg and sperm, the gametes. 3. Formation of body (somatic) cells by nuclear division is mitosis. 4. Mitosis delivers chromosomes and their DNA to the cell lineage. 5. Although the cell lineage differentiates, the genes not expressed are still present. 6. Mitosis ensures the equality of genetic material. 7. In animals that reproduce asexually, mitosis transfers genetic information to progeny. 8. In animals that reproduce sexually, parents produce sex cells (known as gametes or germ cells) with half the number of chromosomes. a. This prevents the union of gametes from doubling the number of parental chromosomes. b. This requires reduction division or meiosis. B. Structure of Chromosomes 1. Chromatin a. DNA in eukaryotic cells occurs in strands of chromatin.. b. Chromatin is a complex of DNA with histone and nonhistone proteins. c. Chromatin is organized into a number of discrete linear bodies called chromosomes. 2. Chromosomes a. Chromosomes stain deeply with biological dyes. b. They are of set but varied lengths. c. A species will have a specific number of chromosomes in all cells except gametes. d. During mitosis, chromosomes shorten further; they are constricted at the centromere, which is the location of the kinetochore. (Figure 3.21) e. DNA packaging allows the cell to fit long strands of DNA into the small nuclear space; however, when the DNA is packaged it is not accessible. C. Phases in Mitosis 1. Cell division involves division of nuclear chromosomes (mitosis) and cytoplasm (cytokinesis). a. When a nucleus divides without cytokinesis, a multinucleate cell results. b. When several cells fuse, they can also form a multinucleate syncytium. 2. Mitosis is a four-step process with each step merging into the next. 3. When the cell is not actively dividing, it is in interphase during which DNA replicates and genes are transcribed. 4. Prophase (Figures 3.22, 3.23) a. In early prophase, centrosomes replicate and the two centrosomes migrate to opposite sides of the nucleus. b. Microtubules form an oval-shaped spindle between the centrosomes. c. Other microtubules radiate outward to form asters. d. Nuclear chromatin condenses into chromosomes; the sister chromatids were actually formed during interphase. e. Spindle fibers reach the centrosome and bind to the kinetochore. 5. Metaphase (Figures 3.22, 3.23) a. Kinetochore microtubule pull condensed sister chromatids to the central metaphasic plate. b. Centromeres line up precisely on the equatorial plate; arms of chromatids dangle. 6. Anaphase (Figures 3.22, 3.23) a. The cohesion proteins that held the chromatids together at the centromere region are now removed. b. Chromosomes move toward their respective poles, pulled by kinetochore microtubules. c. As chromosomes are pulled apart, the centrosomes are moved further so the cell becomes elongated. 7. Telophase (Figures 3.22, 3.23) a. Phase begins as daughter chromosomes reach each pole. b. Spindle fibers disappear. c. Chromosomes lose identity and diffuse into chromatin network in nucleus. d. Nuclear membranes reappear around the two daughter nuclei. D. Cytokinesis: Cytoplasmic Division 1. During the final stage of nuclear division, a cleavage furrow appears on cell surface. 2. Microfilaments of actin just beneath the surface draw the furrow inward. 3. Infoldings edges of cytoskeleton meet and fuse, completing cell division. E. Cell Cycle (Figure 3.24) 1. Cells undergo cycles of growth and replication. 2. A cell cycle is the interval between one cell division and the next. 3. Interphase a. Nuclear division occupies 5–10% of the cell cycle; the rest is interphase. b. Early concepts of interphase as an inactive stage of rest are incorrect. c. DNA replication occurs during interphase. d. S (for synthesis) stage lasts about 6 of the 18–24 hours of a cell cycle in a human. e. Both strands of DNA replicate a complimentary strand. f. The G1 period precedes the S stage; transfer RNA, ribosomes, messenger RNA and enzymes are synthesized. g. The G2 period follows the S stage; spindle and aster proteins form in preparation for chromosome separation. 4. Embryonic Cells a. Embryonic cells divide rapidly with no cell growth between divisions, just subdivision. b. DNA synthesis may be hundreds of times faster in embryonic cells than in adult cells. 5. As organisms develop, the cell cycle of most cells lengthens. a. A non proliferative phase or G0 ends the cycle. b. Neurons do not divide further after birth and are in a permanent G0. 6. Cell Cycle Control (Figure 3.26) a. Regulation of the cell cycle is mediated by cyclin-dependent kinases (cdks). b. Cyclins are activating subunits of cdks. c. Kinase enzymes add phosphate groups to other proteins to activate or inactivate them. d. The passage from one cell cycle to the next is likely regulated by phosphorylation and dephosphorylation of specific cdks and their interaction with phase specific cyclins. 7. Flux of Cells a. Cell division is very rapid during early development of an organism. b. The human infant has 2 trillion cells that originated from one fertilized egg; this represents 42 cell divisions. c. Five more cell divisions produce an adult with 60 trillion cells. d. Various cells divide in days, months or years; muscle and nerve cells stop dividing in childhood or before. e. A human sheds about 1–2% of the total number of cells daily from skin, digestive tract, sperm and short-lived red blood cells. 8. Apoptosis a. Apoptosis is programmed cell death. b. Apoptosis is in many cases necessary for continued health and development of an organism. c. Cells shrink, fragment, and then the remains are taken up by surrounding cells. Lecture Enrichment 1. The ability of early microscopists to see cell structures is amazing. Slides or overhead transparencies of Leeuwenhoek’s primitive single lens device, each made to accommodate another view, help illustrate the difficulty of working with primitive instruments. The Golgi apparatus was at the limit of light microcopy resolution and is a tribute to his microscopic ability, as was his neuron preparations. Ask students to consider how research had to await better microscope technology and different staining methods to allow smaller structures to be examined. 2. Clarify the difference between magnification (making something appear larger) and resolution (distinguishing between two adjacent structures). 3. Show scanning electron micrographs of a freeze fractured plasma membrane. Ask students to determine which face is the cytoplasmic and which the external side of the membrane; proteins are more frequent in the cytoplasmic face. Ask why that would be so. 4. Most students have seen an oil slick on a water puddle. If we measure the volume of oil, measuring the surface area of the slick and dividing this into the volume determines the molecular size. With this information, ask students how they could show that the cell membrane lipid bilayer is a two-layer fluid. 5. While it is a congealed colloidal mass rather than a lipid bilayer, hot chocolate scum can be used as an example of a “membrane” that forms from natural physical laws without any vitalistic forces. 6. The term “cholesterol” has a generally bad connotation. Describe the function of cholesterol in the plasma membranes of animal cells, and ask why it is missing in plant cells. There are other lipids that serve the same function in plant membranes. 7. The immense diversity of proteins that are embedded in or attached to the plasma membrane have a wide array of different functions in the animal kingdom, and determine cell and tissue “identity.” Ask why these membrane-associated proteins are also found in membrane-bound organelles such as vesicles, vacuoles and mitochondria. Compare how they function there with their function in the plasma membrane. 8. At the start of class, place dialysis bags containing various molar solutions of saline in beakers of differing molar solutions. Examine at the end of class and determine which beakers represent a cell in hypotonic, hypertonic, or isotonic solutions. Commentary/Lesson Plan Background: Most students have some experience working with a microscope, although the movement toward using a microscope-mounted television camera to demonstrate slides may remove this critical experience from students’ hands. Providing microscopic or photographic images is critical for students to visualize most cell components. This chapter is also heavily laden with cell structure terminology and chemical concepts that may not be in all students’ backgrounds. Visuals and demonstrations are critical to understanding most membrane properties. Clear examples of hypotonic, hypertonic, and isotonic solutions—explained in relationship to the external solution—are critical even for biology students with previous exposure. Misconceptions: Students may have many mistaken beliefs relative to this section: Cellular life is too complex to be explained by laws of physics and chemistry. Genetic coding for all cell structures is only in the nuclear DNA. Cholesterol is always bad. No reproductive cell processes are occurring during interphase. Stages of mitosis are distinct or noncontinuous and jerkily move from one stage to another. We must keep all the cells we produce; cell loss is bad. Life is always good. Death is always bad. Schedule: HOUR 1 3.1. Cell Concept A. History B. Cell Theory C. How Cells Are Studied 3.2. Cell Organization: Complex Organelles and Energy Transformations A. Prokaryotic and Eukaryotic Cells B. Major Components of Eukaryotic Cells and Their Functions C. Cell Membrane D. Nucleus E. Endoplasmic reticulum F. Lysosomes G. Contractile Vacuoles H. Mitochondria I. Cytoskeleton J. Surfaces of Cells and Their Specializations HOUR 2 3.3. Membrane Function A. Plasma Membrane; Dynamic and Selective B. Cell Membrane Function C. Diffusion and Osmosis D. Diffusion through Channels E. Carrier-Mediated Transport F. Endocytosis G. Exocytosis HOUR 3 3.4. Mitosis and Cell Division A. Cell Types B. Structure of Chromosomes C. Phases in Mitosis D. Cytokinesis: Cytoplasmic Division E. Cell Cycle ADVANCED CLASS QUESTIONS: 1. “Vitalism” is the mistaken belief that additional vital forces beyond the normal laws of chemistry and physics are necessary to explain life and movement inside cells. Why are modern biologists not vitalists? Answer: Modern biologists are not vitalists because they recognize that all biological phenomena, including those that occur within cells, can be explained by the principles of chemistry and physics without the need for additional vital forces. Several key reasons why modern biologists reject vitalism include: 1. Chemical and Physical Basis of Life : Modern biology is founded on the principle that life processes can be understood in terms of the chemical and physical properties of biological molecules and the interactions between them. The discovery of the structure and function of DNA, proteins, and other biological molecules has provided a detailed understanding of how living organisms function at the molecular level. 2. Experimental Evidence : Advances in biochemistry, molecular biology, and biophysics have provided extensive experimental evidence supporting the idea that all biological phenomena, including metabolism, growth, development, and movement within cells, can be explained by the principles of chemistry and physics. These experiments have demonstrated that biological processes are governed by the same physical and chemical laws that govern non-living matter. 3. Emergence : Modern biology recognizes the concept of emergence, which states that complex biological properties and phenomena, such as consciousness, self-organization, and cellular processes, emerge from the interactions of simpler components at lower levels of organization. This emergent behavior does not require the invocation of vital forces beyond the laws of chemistry and physics. 4. Reductionism : Modern biology adopts a reductionist approach, which seeks to explain complex biological phenomena by breaking them down into simpler, more fundamental components. This reductionist approach has been highly successful in explaining many aspects of biology, including cellular processes, in terms of the interactions of individual molecules. 5. Consistency with Scientific Method : Vitalism is not consistent with the principles of the scientific method, which requires that scientific hypotheses be testable and falsifiable. The idea of vital forces is not testable or falsifiable and therefore does not meet the criteria for scientific validity. In summary, modern biologists reject vitalism because they recognize that all biological phenomena, including those that occur within cells, can be explained by the principles of chemistry and physics without the need for additional vital forces. The extensive experimental evidence supporting this view, along with the success of reductionist approaches in explaining complex biological phenomena, has led to the rejection of vitalism in modern biology. 2. Why are syncytial and multinucleate tissues not a violation of the cell theory? Answer: Syncytial and multinucleate tissues are not a violation of the cell theory because they still adhere to the fundamental principles of the cell theory, despite having multiple nuclei within a single cytoplasmic mass. The cell theory states: 1. All living organisms are composed of one or more cells. 2. The cell is the basic unit of structure and function in organisms. 3. All cells arise from pre-existing cells. Syncytial and multinucleate tissues, such as those found in skeletal muscle fibers and certain fungal hyphae, do not violate these principles for the following reasons: 1. Composition of Living Organisms : Syncytial and multinucleate tissues are still composed of cells, even though they may contain multiple nuclei within a single cytoplasmic mass. Each nucleus within the syncytium controls specific regions of the cytoplasm and performs specific functions, similar to individual cells. 2. Basic Unit of Structure and Function : Despite having multiple nuclei, syncytial and multinucleate tissues still function as the basic units of structure and function. For example, skeletal muscle fibers contain multiple nuclei but still function as a single unit to contract and generate force. 3. Cellular Origin : Syncytial and multinucleate tissues still adhere to the principle that all cells arise from pre-existing cells. During development, these tissues are formed by the fusion of multiple individual cells or by the division of a single cell without cytokinesis. In summary, syncytial and multinucleate tissues do not violate the cell theory because they still consist of cells, function as the basic units of structure and function, and arise from pre-existing cells. Despite having multiple nuclei within a single cytoplasmic mass, these tissues adhere to the fundamental principles of the cell theory. 3. Why does the electron microscope have greater resolving power than the light microscope? Answer: The electron microscope has greater resolving power than the light microscope due to several key factors: 1. Wavelength of Illumination : • In light microscopy, the resolution is limited by the wavelength of visible light, which ranges from 400 to 700 nanometers. This limits the ability to distinguish between two closely spaced objects. • In contrast, electron microscopes use a beam of electrons with a much shorter wavelength, typically ranging from 0.005 to 0.0025 nanometers. The shorter wavelength of electrons allows for much greater resolution compared to light microscopy. 2. Magnification : • Electron microscopes can achieve much higher magnifications compared to light microscopes. While light microscopes typically have a maximum magnification of around 1000x to 2000x, electron microscopes can achieve magnifications of up to 2 million times. • Higher magnification allows for the visualization of smaller structures and details, further enhancing the resolving power of the electron microscope. 3. Use of Electromagnetic Lenses : • Electron microscopes use electromagnetic lenses to focus the electron beam, allowing for much greater control and precision compared to the glass lenses used in light microscopes. • The electromagnetic lenses used in electron microscopes can produce much smaller focal spots, resulting in higher resolution images. 4. Detection System : • Electron microscopes use specialized detectors to capture images formed by the interaction of electrons with the specimen. These detectors are capable of detecting the scattered electrons with high sensitivity, allowing for the visualization of fine details. • In contrast, light microscopes rely on optical lenses and photomultiplier tubes to capture images formed by the interaction of light with the specimen, which limits their resolution. In summary, the electron microscope has greater resolving power than the light microscope due to its use of electrons with a shorter wavelength, higher magnification capabilities, use of electromagnetic lenses, and specialized detectors capable of capturing high-resolution images. These factors allow electron microscopes to visualize much smaller structures and details than light microscopes. 4. Plants have rigid walls; thus freezing and thawing of vegetables destroys these structures as small sharp ice crystals pierce them. While meat lacks cell walls and we do not notice additional “limpness” after repeated thawing, it still produces the bad taste of “freezer burn.” What organelle is involved in this autodigestion? How would this concept affect the plans of individuals who schedule themselves to be frozen immediately after death in hopes of being thawed out and cured at some future date? Answer: The organelle involved in autodigestion is the lysosome. Lysosomes contain hydrolytic enzymes that can break down cellular components, including proteins, lipids, and nucleic acids. When cells are damaged, lysosomes may rupture, releasing these enzymes, which then degrade cellular structures, leading to autodigestion. This concept would greatly affect the plans of individuals who schedule themselves to be frozen immediately after death in hopes of being thawed out and cured at some future date. Even if these individuals were to be successfully thawed out in the future, their cells would likely undergo extensive damage due to lysosomal autodigestion, making revival and cure highly unlikely. 5. Life begins at the cellular level of organization. Which organelles contribute to the ability of the cell to maintain its structure and grow? What are the functions of these organelles? Answer: Organelles that contribute to the ability of the cell to maintain its structure and grow include the endoplasmic reticulum (ER), Golgi apparatus, and ribosomes. • Endoplasmic reticulum (ER): The ER is involved in protein synthesis and lipid metabolism. It provides a large surface area for various cellular activities. The rough ER is studded with ribosomes and is involved in protein synthesis, while the smooth ER is involved in lipid metabolism and detoxification. • Golgi apparatus: The Golgi apparatus modifies, sorts, and packages proteins and lipids into vesicles for delivery to targeted destinations. • Ribosomes: Ribosomes are responsible for protein synthesis. They translate the genetic code from mRNA into a specific sequence of amino acids to form a protein. 6. Why are sugar residues of glycoproteins and glycolipids located only on the outside face of the plasma membrane? How are these residues important in cellular recognition? Answer: Sugar residues of glycoproteins and glycolipids are located only on the outside face of the plasma membrane because the enzymes that attach the sugar residues to these molecules are located in the lumen of the Golgi apparatus. As proteins and lipids pass through the Golgi apparatus, they are modified by the addition of sugar residues. Once these molecules reach the outer face of the plasma membrane, they are glycosylated.These sugar residues are important in cellular recognition because they form glycoprotein and glycolipid complexes on the cell surface that act as identification tags. These complexes are involved in cell-cell recognition, cell adhesion, and cell signaling. 7. Ask a student to trace the pathway a protein molecule takes through the endomembrane system from its production on the rough ER to release from a vesicle at the cell’s surface. Would the pathway be different if the protein were made on a free ribosome? Answer: If a protein molecule is produced on the rough endoplasmic reticulum (ER), it follows this pathway through the endomembrane system: 1. The protein is synthesized on ribosomes attached to the rough ER. 2. It enters the lumen of the rough ER, where it undergoes folding and post-translational modifications. 3. Vesicles bud off from the rough ER, carrying the protein to the Golgi apparatus. 4. In the Golgi apparatus, the protein undergoes further processing, such as glycosylation and sorting. 5. The protein is then packaged into vesicles and transported to the cell membrane. 6. The vesicle fuses with the cell membrane, releasing the protein to the cell's exterior. If the protein were made on a free ribosome, it would not enter the endomembrane system. Instead, it would remain in the cytoplasm, where it would carry out its function within the cell. 8. Compare the functions of the different kinds of junctions that hold cells together and what kinds of cells they would be likely to link. Answer: Different kinds of junctions that hold cells together include tight junctions, desmosomes, and gap junctions. • Tight junctions: Tight junctions form a barrier that prevents the leakage of material between cells. They are found in epithelial tissues and are important for maintaining the integrity of the tissue. Tight junctions would be likely to link cells in tissues that need to maintain a barrier, such as the epithelium lining the intestine. • Desmosomes: Desmosomes are spot-like junctions that provide mechanical strength to tissues by anchoring cells together. They are found in tissues that experience mechanical stress, such as skin and heart muscle. • Gap junctions: Gap junctions allow for the direct passage of small molecules and ions between cells. They are found in tissues that require rapid communication, such as cardiac muscle and smooth muscle. 9. You can “peel” a raw egg without breaking the membrane. If you place the shell-less egg in a glass of water, it will swell to the size of an orange. Why is the flow one way? Answer: The flow of water into the shell-less egg is due to osmosis. When the egg is placed in a glass of water, water molecules move from an area of higher water concentration (outside the egg) to an area of lower water concentration (inside the egg) through the semipermeable membrane of the egg. The egg swells to the size of an orange because the concentration of solutes inside the egg is higher than the concentration of solutes in the water. As water moves into the egg, the volume of the egg increases, causing it to swell. CHAPTER 4 CELLULAR METABOLISM CHAPTER OUTLINE 4.1 Deferring the Second Law (Figure 4.1) A. Living systems seem to contradict the second law of thermodynamics 1. The second law of thermodynamics states that the amount of energy in a closed system decreases. 2. Living organisms are not closed systems. 3. Living organisms only borrow energy ultimately created by the sun to grow and maintain themselves. 4. The increase in the molecular orderliness of living systems appears to contradict the second law of thermodynamics. 5. However, in order to increase its molecular orderliness, it reduces the molecular orderliness of a much larger amount of food. 6. Continuous provision of additional food is only possible from the sun’s continual input. 7. Eventually the orderly structure of the organism will end at death; entropy wins out. 8. Cellular metabolism is the collective total chemical processes that maintain living cells. 4.2. Energy and the Laws of Thermodynamics 1. Energy exists in two states. a. Kinetic energy is energy of motion. b. Potential energy is stored energy; it is not doing work but has the capacity to do work. 2. The two laws of thermodynamics govern conversion of energy from one form to another. a. First law of thermodynamics: energy cannot be created or destroyed but it can be changed from one form to another. b. Second law of thermodynamics: a closed system moves toward increasing disorder or entropy but living systems maintain and increase their organization as energy enters from the sun. (Figure 4.2) 3. Free energy is the amount of energy that is free to do work after a chemical reaction; it is energy present in chemical bonds minus energy that cannot be used. 4. In cells, most reactions are exergonic reactions that release free energy; they are spontaneous and proceed “downhill.” 5. In cells, some important reactions are endergonic reactions that require free energy; they must be “pushed uphill.” 6. ATP is an important molecule that powers many endergonic reactions. 4.3. Role of Enzymes A. Enzymes and Activation Energy (Figure 4.3) 1. In any reaction, exergonic or endergonic, chemical bonds must be destabilized for the reaction to proceed. 2. Activation energy must be provided to break a bond; this is done by catalysts or by raising the temperature. 3. Enzymes are catalysts that reduce the amount of activation energy required for a reaction, making it more likely but not altering the change in free energy. B. Nature of Enzymes 1. Enzymes vary from small to large molecules; some are pure proteins. 2. Some enzymes require nonprotein cofactors to perform enzymatic functions. 3. Organic cofactors are called coenzymes; they are derived from vitamins in the diet. 4. RNA is now known to possess enzymatic activity. C. Action of Enzymes (Figure 4.4) 1. Every enzyme is specific in its action; it has a unique molecular configuration and active site to catalyze only one specific reaction. 2. A substrate is a reactant in an enzymatic reaction. 3. The enzyme binds to substrate to form an enzyme-substrate complex for a brief moment. 4. Proof of the brief enzyme-substrate complex state is that at high substrate concentration, all catalytic sites may be filled for a brief time. 5. Conversion of glucose to carbon dioxide requires 19 reactions, each with a specific enzyme. D. Specificity of Enzymes (Figure 4.5) 1. Specificity of enzyme and substrate means that no useless by-products are formed. 2. Most enzymes take on only one substrate at a time; a few will act on many proteins. 3. Some enzymes will repeat the catalysis billion of times until worn out. 4. Some enzymes undergo catalytic cycles at speed of a million cycles per minute. E. Enzyme-Catalyzed Reactions 1. Enzyme-catalyzed reactions are reversible but most reactions are in one direction. 2. Some enzymes degrade proteins (catabolism) and other enzymes synthesize them (anabolism). 3. Net direction of a chemical reaction depends on relative energy contents of substances involved. 4. Many enzymes are repeatedly activated and inactivated and several mechanisms for regulating enzyme activities are well known. F. Enzyme Regulation (Figure 4.6) 1. Many enzymes act reversibly: synthesis or degradation may result 2. If an enzyme converts A to B and B is removed, enzyme will tend to restore the ratio of B to A. 3. Genes may switch enzymes on or off; some molecules alter the shape of enzymes, and enzymes may have active and inactive forms. 4.4. Chemical Energy Transfer by ATP (Figures 4.7, 4.8) A. Coupled Reactions 1. Coupled reactions occur when energy released by an exergonic reaction is used to drive an endergonic reaction. 2. Energy released from ATP ––––> ADP + P is central to many biological reactions. 3. ATP breakdown is coupled to a reaction that requires energy; both reactions take place at the same time in the same place. 4. The bond energy released in the reaction is transferred to ADP + P which becomes ATP. 5. ATP is an energy-coupling agent and not a fuel; it is formed as needed and therefore metabolism is mostly self-regulating. (Figure 4.9) 4.5. Cellular Respiration A. Electron Transport Traps Chemical Bond Energy 1. All cells obtain their chemical energy requirements from oxidation-reduction reactions. 2. In oxidation-reduction (redox) reactions, electrons pass from one molecule to another. 3. Oxidation is the loss of electrons. 4. Reduction is the gain of electrons. 5. Both reactions occur at the same time because one molecule accepts electrons given up by another molecule. (Figure 4.10) 6. When the oxidized agent accepts electrons, energy is liberated as electrons move to a more stable position. 7. As electrons move through a series of carriers, each carrier is reduced by accepting electrons and reoxidized by passing electrons to the next carrier. 8. Gradual release of energy ensures a maximum yield of ATP. 9. Electrons are ultimately transferred to a final electron acceptor. B. Aerobic Versus Anaerobic Metabolism 1. Oxygen is the final electron acceptor in aerobes 2. Anaerobic metabolism employs some other final electron acceptor. 3. Evolution has favored aerobic metabolism because it is more efficient. 4. Complete oxidation of glucose releases nearly 20 times more energy; therefore less food is required to maintain metabolism. C. Overview of Respiration (Figure 4.11) 1. Oxidation of fuel molecules is removal of electrons, not direct combination of oxygen with fuel. 2. Hans Krebs described three stages of complete oxidation of fuel molecules. 3. Stage I -digestion, the breakdown of large molecules to smaller ones in intestinal tract, does not yield useful energy. 4. In Stage II, also known as glycolysis, most foodstuffs are degraded into two 3-carbon units (pyruvic acid), but little ATP is generated. 5. In Stage III, food undergoes final oxidation until electrons are accepted by molecular oxygen to form water, with a large yield of ATP. D. Glycolysis (Figure 4.12) 1. Addition of two phosphate groups activates glucose. 2. Two separate reactions use two ATP. 3. Glucose, a C6 molecule, splits into two C3 (pyruvic acid) fragments. 4. Two electrons and one hydrogen ion are accepted by NAD+ and result in two NADH. 5. Enough energy is released from breakdown of glucose to generate four ATP molecules. 6. Two of four ATP molecules produced are required to replace two ATP molecules used in the phosphorylation of glucose. 7. There is a net gain of two ATP from glycolysis. 8. Glucose + 2ADP + 2Pi + 2NAD+ ––––> 2 pyruvic acid + 2NADH + 2ATP E. Acetyl-CoA: Strategic Intermediate in Respiration (Figure 4.13) 1. The two molecules of pyruvic acid enter a mitochondrion. 2. Each is oxidized; one molecule of carbon dioxide is released. 3. The 2-carbon residue condenses with coenzyme A to form acetyl coenzyme A (acetyl-CoA). F. Krebs Cycle: Oxidation of Acetyl-CoA (Figure 4.14) 1. Degradation of the 2-carbon acetyl group of acetyl-CoA occurs in the Krebs cycle. 2. Acetyl coenzyme A condenses with a 4-carbon acid releasing coenzyme A to react again. 3. A series of reactions releases the two carbons as carbon dioxide; oxaloacetic acid is regenerated. 4. Hydrogen ions and electrons in the oxidations are transferred to NAD and FAD; a pyrophosphate bond is generated in guanosine triphosphate. 5. The high-energy phosphate transfers to ADP to form ATP. 6. Acetyl unit + 3NAD+ + FAD + ADP + Pi ––––> 2CO2 + 3NADH + FADH2 + ATP 7. 11 molecules of ATP are formed; other molecules are reactants and recycled products. G. Electron Transport Chain (Figure 4.15) 1. High-energy electrons are delivered to the protein-based system and low-energy electrons leave it. 2. The H+ gradient produced drives the synthesis of ATP. 2. Reduced FAD from the Krebs cycle enters the electron transport chain at a lower level than NADH and yields two ATP molecules. 3. ATP production is tied to a proton (H+) gradient across membranes; this is called chemiosmotic coupling. H. Efficiency of Oxidative Phosphorylation (Figure 4.16; Table 4.1) 1. Glucose + 2 ATP + 36 ADP + 36 P + 6 O2 ––––> 6 CO2 + 2 ADP + 36 ATP + 6 H2O 2. Cytoplasmic NADH from glycolysis requires one molecule of ATP to fuel transport of each NADH into mitochondria. 3. Net yield may be as high as 36 molecules of ATP per glucose molecule. 4. Efficiency of aerobic oxidation is 38%; human-designed systems seldom exceed 5–10% efficiency. 5. The inner foldings of the cristae of the mitochondria increase surface area thereby increasing production of ATP. (Table 4.1) I. Anaerobic Glycolysis: Generating ATP Without Oxygen (Figure 4.17) 1. In absence of molecular oxygen, oxidation of pyruvic acid cannot occur; consequently, most animals reduce pyruvic acid to lactic acid, which becomes the final electron acceptor. 2. In alcoholic fermentation, one pyruvic acid carbon is released as carbon dioxide and the resulting 2-carbon compound is reduced to ethanol. 3. This provides some high-energy phosphate in situations where oxygen is depleted. 4. Animals reduce pyruvate to lactate when it is produced faster than the Krebs cycle can oxidize it. 5. When blood cannot remove all lactate from muscles, the lactate changes pH and causes muscles to fatigue and the animal is in oxygen debt because oxygen is still needed after exercising. 6. Diving birds and salmon need muscular bursts in the absence of oxygen. 7. Some parasitic animals have dispensed with oxidative phosphorylation. 4.6. Metabolism of Lipids (Figure 4.18) A. Breakdown of a Triglyceride 1. The first step in breakdown of a triglyceride is hydrolysis of glycerol and fatty acid molecules. 2. Glycerol is phosphorylated and enters the glycolytic pathway. 3. The remainder is fatty acids; stearic acid is common. 4. Long hydrocarbon chains are sliced by oxidation of two carbons at a time. 5. Complete oxidation of 1 stearic acid nets 146 ATP molecules; glucose nets 108 ATP molecules. B. Fat Stores 1. Fat stores are concentrated fuels. 2. Fats contain almost pure hydrocarbons. 3. Acetyl coenzyme A is a source of carbon atoms to build fatty acids; carbohydrates, fats, and proteins that can be degraded to acetyl coenzyme A. 4. Most usable fat is in adipose tissue; women average 30% more fat than men. 5. Many researchers are now investigating the physiological and psychological aspects of obesity. 6. There is increasing evidence that food intake and feeding centers located in the brain regulate the amount of fat deposition. 7. There is also evidence that there is a genetic composition to obesity. 8. To combat obesity, drugs are being developed that act on the different stages of lipid metabolism. 4.7. Metabolism of Proteins (Figure 4.19) A. Amino Acids 1. Each of the 20 amino acids requires a separate pathway for synthesis and degradation. 2. Tissues use the amino acid pool, in the blood and extracellular fluid, as a source of molecules. 3. Excess proteins serve as fuel just like carbohydrates and fats; carnivores get nearly half of their high-energy phosphate from amino acid oxidation. 4. Nitrogen is removed from amino acids by deamination; carbon skeletons then enter regular routes of metabolism. 5. The other product of deamination is toxic ammonia; aquatic animals excrete it directly but terrestrial animals must convert it to less toxic urea or uric acid. 6. Uric acid is insoluble allowing removal in solid form; desert animals that need to conserve water use it. Lecture Enrichment 1. Describe how life can be so organized when the level of entropy in the universe continues to increase. The universe as a whole is “running down,”—an individual cell, organism or ecosystem must be considered as an open system that requires a continuous energy input from outside to maintain its organization: islands of organization in a sea of entropy. This is a critical concept to counter the misunderstanding promoted by some creationists that entropy prevents evolution. 2. Demonstrate using reactions or visuals conveying how an enzyme can lower the activation energy for a reaction and why there is an energy of activation even for a spontaneous reaction. 3. Discuss why vitamins are required only in small amounts and how they are active in the cell. 4. Explain how coupled reactions using ATP allow reactions that require energy input to take place in the cell under conditions that are compatible with life. 5. Trace the flow of carbon molecules throughout the pathways of glycolysis and cellular respiration, focusing on where they enter and leave each set of reactions. 6. Do the same with hydrogen atoms, and be sure to show that some of the hydrogen atoms being carried off by NADH and FADH2 are coming from water and are not just the remnants of the glucose. Water can be placed on both sides of the general equation for cellular respiration to account for this entry of water into the process. 7. Point out the chemical relationships between photosynthesis and cellular respiration; note that these are complementary processes that are part of the interrelatedness of all life and the cyclic renewal of reactants and products. 8. Compare the production of ATP through chemiosmotic phosphorylation in the mitochondrion and the chloroplast. 9. Discuss how the production and breakdown of ATP must be cyclic and extremely rapid to allow the many chemical reactions to occur. Note the limits on the production of ATP (must have ADP and phosphate) and how recycling of these materials must take place across the outer membrane of the mitochondrion. 10. Cyanide stops the cytochrome system of electron transport. This explains why cyanide is a universal poison effective in all organisms with mitochondria. Commentary/Lesson Plan Background: Limited high school physics coursework among U.S. students means that the concepts of kinetic and potential energy may be introduced in this course. Catalysts and enzymes may also be a new chemical concept. Students weak in chemistry will also find NAD, FAD, ATP, etc. to be rather meaningless alphabet soup to be memorized without understanding. However, many students will have some understanding of lactic acid and the concept of oxygen debt due to their involvement in sports. “Fat” has a negative connotation; it will be difficult to establish with students that some level of fat storage is necessary for healthy life following birth. Misconceptions: The concept of entropy is often misunderstood from its popularized but incorrect treatment in the press (i.e., a desk becoming disorderly is not entropy). “Respiration” is commonly used not only for cellular respiration but also for the breathing process that is better called “ventilation.” Early clarification will help avoid confusion. Many students will not understand the catalyst concept and believe all reactions must “use up” reactants. High school texts often only use the example of sugar in respiration; many students will not recognize that larger molecules are also broken down for energy. ATP is often taught as a long-term energy storage molecule. Schedule: HOUR 1 4.1 Energy and the Laws of Thermodynamics A. Metabolism and the Second Law B. Free Energy HOUR 2 4.2. Role of Enzymes A. Enzymes and Activation Energy B. Nature of Enzymes C. Action of Enzymes D. Specificity of Enzymes E. Enzyme-Catalyzed Reactions F. Enzyme Regulation HOUR 3 4.3. Chemical Energy Transfer by ATP A. Coupled Reactions 4.4. Cellular Respiration A. Electron Transport Traps Chemical Bond Energy B. Aerobic Versus Anaerobic Metabolism C. Overview of Respiration D. Glycolysis E. Acetyl-CoA: Strategic Intermediate in Respiration F. Krebs Cycle: Oxidation of Acetyl Coenzyme A G. Electron Transport Chain H. Efficiency of Oxidative Phosphorylation I. Anaerobic Glycolysis: Generating ATP Without Oxygen HOUR 4 4.5. Metabolism of Lipids A. Breakdown of a Triglyceride B. Fat Stores 4.6. Metabolism of Proteins A. Amino Acids ADVANCED CLASS QUESTIONS: 1. What are the advantages to having individual steps in a metabolic pathway? Answer: Individual steps in a metabolic pathway offer several advantages: 1. Regulation : Each step in a metabolic pathway can be independently regulated, allowing the cell to control the overall flux through the pathway according to its needs. 2. Energy Efficiency : Breaking down complex processes into smaller steps allows for better energy efficiency. Energy released in one step can be captured and used to drive subsequent steps. 3. Prevention of Buildup : By breaking down molecules step by step, the cell can prevent the buildup of potentially harmful intermediates. 4. Substrate Specificity : Each step in a metabolic pathway is typically catalyzed by a specific enzyme, ensuring that only the appropriate substrates are converted into products. 5. Facilitation of Anabolic and Catabolic Pathways : Metabolic pathways often involve both anabolic (building up) and catabolic (breaking down) processes. By breaking these processes into individual steps, the cell can efficiently coordinate both types of reactions. 2 What way does glycolysis demonstrate the unity of living things and support the theory of evolution? Answer: Glycolysis, the metabolic pathway that converts glucose into pyruvate, demonstrates the unity of living things and supports the theory of evolution in several ways: 1. Conservation of Metabolic Pathways : Glycolysis is found in nearly all living organisms, from simple bacteria to complex multicellular organisms. The presence of this highly conserved pathway across diverse species demonstrates the unity of life and suggests a common evolutionary origin. 2. Evolutionary Adaptation : While the overall process of glycolysis is conserved, individual steps can vary slightly among different organisms. These variations reflect evolutionary adaptations to different environmental conditions, such as the availability of oxygen or different energy requirements. 3. Evidence of Ancient Origin : Glycolysis is thought to be one of the most ancient metabolic pathways, predating the evolution of oxygenic photosynthesis. Its widespread occurrence across all domains of life suggests that it evolved very early in the history of life on Earth. 4. Survival Advantage : Glycolysis provides organisms with a mechanism to generate energy (in the form of ATP) from glucose, a simple sugar that can be readily obtained from the environment. Organisms that were able to efficiently utilize glucose through glycolysis would have had a survival advantage, leading to its widespread adoption and conservation throughout evolutionary history. In summary, the widespread presence and conservation of glycolysis across all living organisms provide strong evidence for the unity of life and support the theory of evolution by demonstrating how fundamental metabolic pathways have evolved and been conserved over billions of years. 3. Why does the growth of a baby into a 100 pound adult not violate the second law of thermodynamics? Answer: The growth of a baby into a 100-pound adult does not violate the second law of thermodynamics because the increase in the baby's mass is not a spontaneous process; it requires energy input. The second law of thermodynamics states that in any energy transfer or transformation, the total entropy (or disorder) of a closed system will always increase over time. In the case of a growing baby, the increase in mass is achieved by consuming food and utilizing the energy stored within the food molecules. This energy is used to build new tissues, organs, and ultimately increase the baby's mass. Thus, the process of growth in a baby into a 100-pound adult involves the conversion of food (chemical energy) into body mass, and it obeys the second law of thermodynamics because it requires an input of energy to decrease entropy locally (by increasing the order and complexity of the baby's body) while increasing entropy in the surrounding environment. 4. What are the key organelles that allow energy to flow through living systems? Answer:The key organelles that allow energy to flow through living systems are: 1. Mitochondria : Mitochondria are often referred to as the "powerhouses" of the cell because they are responsible for producing the majority of the cell's energy in the form of adenosine triphosphate (ATP) through the process of cellular respiration. 2. Chloroplasts : Chloroplasts are organelles found in plant cells and some other eukaryotic organisms. They are the site of photosynthesis, where light energy is converted into chemical energy in the form of glucose. These organelles are crucial for capturing, storing, and utilizing energy in living systems, allowing it to flow through various metabolic pathways. 5. Focusing on the rough ER and Golgi apparatus, why does a cell need energy to maintain its organization. Answer:A cell needs energy to maintain its organization because of the roles played by the rough endoplasmic reticulum (ER) and the Golgi apparatus in protein synthesis, processing, and sorting. 1. Rough Endoplasmic Reticulum (ER) : The rough ER is studded with ribosomes, making it the primary site for protein synthesis in the cell. Newly synthesized proteins are translocated into the lumen of the rough ER, where they undergo folding and initial post-translational modifications. • Energy Requirement : Protein synthesis is an energy-intensive process. The cell needs to continuously supply energy in the form of adenosine triphosphate (ATP) to support the synthesis and translocation of proteins into the rough ER. 2. Golgi Apparatus : The Golgi apparatus receives proteins from the rough ER and modifies them further by adding carbohydrates (glycosylation) or other molecules. It also sorts and packages these modified proteins into vesicles for transport to their final destinations, either within the cell or outside of it. • Energy Requirement : The Golgi apparatus requires energy to carry out the processes of protein modification, sorting, and vesicle trafficking. ATP is needed to power the molecular machinery responsible for these activities. Therefore, to maintain the organization of cellular structures such as the rough ER and Golgi apparatus, the cell needs a constant supply of energy in the form of ATP to support the synthesis, processing, and sorting of proteins within these organelles. 6. A cell gives off heat. Why would you expect both parts of the ATP cycle to be responsible for the loss of useful energy through heat? Answer: Both parts of the ATP cycle are responsible for the loss of useful energy through heat because energy is required to both synthesize ATP (an endergonic process) and to hydrolyze ATP to ADP and inorganic phosphate (an exergonic process). 1. ATP Synthesis (Endergonic Reaction) : During cellular respiration, energy from the breakdown of glucose is used to phosphorylate adenosine diphosphate (ADP), converting it into adenosine triphosphate (ATP) in a process called oxidative phosphorylation. This synthesis of ATP is an endergonic reaction, requiring an input of energy. • Loss of Energy as Heat : Some of the energy released during cellular respiration is lost as heat due to the inefficiencies of the process. This heat energy is a byproduct of ATP synthesis. 2. ATP Hydrolysis (Exergonic Reaction) : When ATP is hydrolyzed to ADP and inorganic phosphate, energy is released. This hydrolysis reaction is exergonic, meaning it releases energy. • Loss of Energy as Heat : However, not all the energy released during ATP hydrolysis is used for cellular work. Some of it is also lost as heat due to the inefficiencies of cellular processes. Therefore, both parts of the ATP cycle are responsible for the loss of useful energy through heat. While ATP synthesis requires energy input and results in the loss of some energy as heat, ATP hydrolysis releases energy, but again, some of this energy is lost as heat. Thus, the overall efficiency of ATP utilization in cellular processes is less than 100%, leading to the generation of heat as a byproduct. 7. Why do most reactions not occur in a cell unless a specific enzyme is present? Answer:Most reactions do not occur in a cell unless a specific enzyme is present due to several reasons: 1. Activation Energy Barrier: Many chemical reactions have high activation energy barriers that must be overcome for the reaction to proceed. Enzymes lower the activation energy required for a reaction to occur, making it easier for the reaction to proceed. 2. Specificity: Enzymes are highly specific in their action, each catalyzing a particular chemical reaction or a group of similar reactions. This specificity ensures that only the desired reaction occurs, preventing wasteful side reactions. 3. Orientation of Substrates: Enzymes provide a specific microenvironment that is conducive to the reaction they catalyze. They bring the substrates together in the correct orientation, which increases the likelihood of a successful reaction. 4. Stabilization of Transition States: Enzymes stabilize the transition state of the reaction, reducing the energy required for the reaction to proceed. This stabilization accelerates the reaction rate. 5. Regulation: Enzyme activity can be regulated in response to cellular conditions, allowing cells to control when and where specific reactions occur. Overall, enzymes play a crucial role in catalyzing and regulating cellular reactions, ensuring that metabolic processes proceed efficiently and without wasteful side reactions. Without enzymes, most cellular reactions would occur too slowly or not at all, making life as we know it impossible. 8. Breaking apart molecules by combination with oxygen is burning. This is a “slow burn” inside of cells. We hear of “spontaneous human combustion.” Some people allege we can burn up from runaway metabolism. Why is it impossible for rapid direct oxidation to originate in the cell environment? Answer: Rapid direct oxidation, such as spontaneous human combustion or runaway metabolism resulting in burning up from within, is impossible in the cell environment due to several reasons: 1. Controlled Environment : Cellular metabolism is highly regulated, and reactions occur in a controlled environment within the cell. Enzymes catalyze metabolic reactions, ensuring that they proceed at an appropriate rate. This regulation prevents the buildup of excessive heat that could lead to burning. 2. Water Content : The human body, like all living organisms, has a high water content. Water is an excellent heat conductor and helps dissipate heat, preventing localized overheating. 3. Efficient Energy Transfer : In cellular metabolism, energy released during oxidation is captured in the form of chemical bonds (such as ATP) rather than being released as heat. This energy is then used for various cellular processes, preventing the buildup of excess heat. 4. Temperature Regulation : The human body maintains a relatively constant internal temperature through mechanisms such as sweating, vasodilation, and shivering. These mechanisms help regulate body temperature and prevent overheating. 5. Physical Limitations : The cell's structure and composition make it physically impossible for rapid direct oxidation to occur. Cellular components, such as membranes and organelles, would be damaged or destroyed by rapid overheating. In summary, the controlled environment, high water content, efficient energy transfer, temperature regulation mechanisms, and physical limitations within the cell environment make it impossible for rapid direct oxidation to originate and lead to burning up from within. Instructor Manual for Integrated Principles of Zoology Cleveland Hickman, Jr., Susan Keen, Allan Larson, David Eisenhour, Helen I'Anson, Larry Roberts 9780073524214
