Cell Biology PDF

Cell Biology What Is a Cell? Cells have all the equipment and expertise necessary to carry out the functions of life. A cell can eat, grow, and move. It can perform necessary maintenance, recycle parts, and dispose of wastes. It can adapt to changes in its environment; and it can even replicate its...

Cell Biology What Is a Cell? Cells have all the equipment and expertise necessary to carry out the functions of life. A cell can eat, grow, and move. It can perform necessary maintenance, recycle parts, and dispose of wastes. It can adapt to changes in its environment; and it can even replicate itself. Despite these similarities, all cells are not equal. Some are truly self-sustaining, as with single-celled bacteria or yeast, whereas others live communally, sometimes as part of complex multicellular organisms. Cells also differ in size. Although cells can be quite large — consider a frog's egg, for example — most are too small to see with the naked eye. Indeed, the development of light microscopy was essential to man's discovery of cells. You won't see the familiar schematic drawings of oval-shaped cells. Real cells are three-dimensional, and they exist in a variety of intricate and remarkable shapes. For instance, a single human nerve cell can be over one meter long, extending from your backbone to your big toe. Compare that with the cells that line your small intestine, which have dozens of tiny, fingerlike projections to maximize the surface area across which nutrients can pass. 2 3 History Cells were first seen in 17th-century Europe with the invention of the compound microscope. In 1665, Robert Hooke referred to the building blocks of all living organisms as "cells" (published in Micrographia) after looking at a piece of cork and observing a cell-like structure; however, the cells were dead. They gave no indication to the actual overall components of a cell. A few years later, in 1674, Anton Van Leeuwenhoek was the first to analyze live cells in his examination of algae. All of this preceded the cell theory which states that all living things are made up of cells and that cells are organisms' functional and structural units. This was ultimately concluded by plant scientist Matthias Schleiden and animal scientist Theodor Schwann in 1838, who viewed live cells in plant and animal tissue, respectively. 19 years later, Rudolf Virchow further contributed to the cell theory, adding that all cells come from the division of pre-existing cells. 4 Cell theory Cell theory is a scientific theory first formulated in the mid-nineteenth century by Theodor Schwann and Matthias Jakob Schleiden: 1. All living organisms are composed of one or more cells 2. The cell is the most basic unit of life In 1855, Rudolf Virchow added the third tenet to cell theory. 3. All cells arise only from pre-existing cells The theory was once universally accepted, but now some biologists consider non-cellular entities such as viruses living organisms, and thus disagree with the first tenet. As of 2021: "expert opinion remains divided roughly a third each between yes, no and don’t know". As there is no universally accepted definition of life, discussion still continues. Modern interpretation of Cell theory The generally accepted parts of modern cell theory include: 1. All known living things are made up of one or more cells. 2. All living cells arise from pre-existing cells by division. 3. The cell is the fundamental unit of structure and function in all living organisms. 4. The activity of an organism depends on the total activity of independent cells. 5. Energy flow (metabolism and biochemistry) occurs within cells. 6. Cells contain DNA which is found specifically in the chromosome and RNA found in the cell nucleus and cytoplasm. 7. All cells are basically the same in chemical composition in organisms of similar species. 5 Techniques But how, exactly, do cells accomplish the complex tasks of life? What tools and materials do they need? And what are the key characteristics that define a cell? Cell biology research looks at different ways to culture and manipulate cells outside of a living body to further research in human anatomy and physiology, and to derive medications. The techniques by which cells are studied have evolved. Due to advancements in microscopy, techniques and technology have allowed scientists to hold a better understanding of the structure and function of cells. Many techniques commonly used to study cell biology are listed: 1- Cell culture Cell culture: Utilizes rapidly growing cells on media which allows for a large amount of a specific cell type and an efficient way to study cells. Cell culture is one of the major tools used in cellular and molecular biology, providing excellent model systems for studying the normal physiology and biochemistry of cells (e.g., metabolic studies, aging), the effects of drugs and toxic compounds on the cells, and mutagenesis and carcinogenesis. It is also used in drug screening and development, and large scale manufacturing of biological compounds (e.g., vaccines, therapeutic proteins). 6  2- Fluorescence microscopy Fluorescent markers such as Green fluorescent protein (GFP), are used to label a specific component of the cell. Afterwards, a certain light wavelength is used to excite the fluorescent marker which can then be visualized. 3- Phase-contrast microscopy Phase-contrast microscopy uses the optical aspect of light to represent the solid, liquid, and gas-phase changes as brightness differences. It is a technique that reveals the hidden details of transparent specimens without staining them. 7  4- Transmission electron microscopy Involves metal staining and the passing of electrons through the cells, which will be deflected upon interaction with metal. This ultimately forms an image of the components being studied. 5- Cytometry Using a flow cytometer machine, cells or other particles suspended in a liquid stream are passed through a laser light beam in single file fashion, and interaction with the light is measured by an electronic detection apparatus as light scatter and fluorescence intensity. Variables that can be measured by cytometric methods include cell size, cell count, cell morphology (shape and structure), cell cycle phase, DNA content, and the existence or absence of specific proteins on the cell surface or in the cytoplasm. 8  6- Cell fractionation This process requires breaking up the cell using high temperature or sonification followed by centrifugation to separate the parts of the cell allowing for them to be studied separately. a method that separates subcellular components and organelles, so that the structures, functions, and molecular compositions of isolated components may be studied. What Defines a Cell? Cells are considered the basic units of life in part because they come in discrete and easily recognizable packages. That's because all cells are surrounded by a structure called the cell membrane — which, much like the walls of a house, serves as a clear boundary between the cell's internal and external environments. The cell membrane is sometimes also referred to as the plasma membrane. Cell membranes are based on a framework of fat-based molecules called phospholipids, which physically prevent water-loving, or hydrophilic, substances from entering or escaping the cell. These membranes are also studded with proteins that serve various functions. Some of these proteins act as gatekeepers, determining what substances can and cannot cross the membrane. Others function as markers, identifying the cell as part of the same organism or as foreign. Still others work like fasteners, binding cells together so they can function as a unit. Yet other membrane proteins serve as communicators, sending and receiving signals from neighboring cells and the environment — whether friendly or alarming. 9 Within this membrane, a cell's interior environment is water based. Called cytoplasm, this liquid environment is packed full of cellular machinery and structural elements. In fact, the concentrations of proteins inside a cell far outnumber those on the outside — whether the outside is ocean water (as in the case of a single-celled alga) or blood serum (as in the case of a red blood cell). Although cell membranes form natural barriers in watery environments, a cell must nonetheless expend quite a bit of energy to maintain the high concentrations of intracellular constituents necessary for its survival. Indeed, cells may use as much as 30 percent of their energy just to maintain the composition of their cytoplasm 10 Biochemical Composition of cells The cellular body is a dense gel-like mixture crowded with proteins made by ribosomes. Therefore, the term cytoplasm implies the correct constitution of the cellular body rather than the term cytosol. As previously mentioned, a cell's cytoplasm is home to numerous functional and structural elements. These elements exist in the form of molecules and organelles — picture them as the tools, appliances, and inner rooms of the cell. Major classes of intracellular organic molecules include nucleic acids, proteins, carbohydrates, and lipids, all of which are essential to the cell's functions. These macromolecules are assembled from building blocks: monosaccharides, fatty acids, amino acids and nucleotides. Nucleic acids are the molecules that contain and help express a cell's genetic code. There are two major classes of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the molecule that contains all of the information required to build and maintain the cell; RNA has several roles associated with expression of the information stored in DNA. Of course, nucleic acids alone aren't responsible for the preservation and expression of genetic material: Cells also 11 use proteins to help replicate the genome and accomplish the profound structural changes that underlie cell division. Proteins are a second type of intracellular organic molecule. These substances are made from chains of smaller molecules called amino acids, and they serve a variety of functions in the cell, both catalytic and structural. For example, proteins called enzymes convert cellular molecules (whether proteins, carbohydrates, lipids, or nucleic acids) into other forms that might help a cell meet its energy needs, build support structures, or pump out wastes. Proteins are encoded by the sequence of nucleic acids in the genetic code. 12 Carbohydrates, the starches and sugars in cells, are another important type of organic molecule. Simple carbohydrates are used for the cell's immediate energy demands, whereas complex carbohydrates serve as intracellular energy stores. Complex carbohydrates are also found on a cell's surface, where they play a crucial role in cell recognition. Chains of monosaccharides can also be plugged onto the other molecule classes forming e.g. glycolipids or glycoproteins. Glycoproteins are also an integral part of the bacterial cell wall and the extracellular matrix in tissues of higher organisms. 13 lipids or fat molecules are components of cell membranes — both the plasma membrane and various intracellular membranes. They are also involved in energy storage, Breaking down fatty acids yields even more energy per mass unit than glucose as well as relaying signals within cells and from the bloodstream to a cell's interior. The relative scale of biological molecules and structures Cells can vary between 1 micrometer (μm) and hundreds of micrometers in diameter. Within a cell, a DNA double helix is approximately 10 nanometers (nm) wide, whereas the cellular organelle called a nucleus that encloses this DNA can be approximately 1000 times bigger (about 10 μm). See how cells compare along a relative scale axis with other molecules, tissues, and biological structures (blue arrow at bottom). Note that a micrometer (μm) is also known as a micron. 14 What Are the Different Categories of Cells? Built from these macromolecules at different scales, two kinds of cells can be discriminated. Rather than grouping cells by their size or shape, scientists typically categorize them by how their genetic material is packaged. Types of Cells prokaryote eukaryote prokaryote If the DNA within a cell is not separated from the cytoplasm. All known prokaryotes, such as bacteria and archaea, are single cells. eukaryote If the DNA is partitioned off in its own membrane-bound room called the nucleus, then that cell is a eukaryote. Some eukaryotes, like amoebae, are free-living, single- celled entities. Other eukaryotic cells are part of multicellular organisms. For instance, all plants and animals are made of eukaryotic cells — sometimes even trillions of them. 15 How Did Cells Originate? Researchers hypothesize that all organisms on Earth today originated from a single cell that existed some 3.5 to 3.8 billion years ago. This original cell was likely little more than a sac of small organic molecules and RNA-like material that had both informational and catalytic functions. Over time, the more stable DNA molecule evolved to take over the information storage function. whereas proteins, with a greater variety of structures than nucleic acids, took over the catalytic functions. The absence or presence of a nucleus is important enough to be a defining feature by which cells are categorized as either prokaryotes or eukaryotes. Scientists believe that the appearance of self-contained nuclei and other organelles represents a major advance in the evolution of cells. But where did these structures come from? More than one billion years ago, some cells "ate" by engulfing objects that floated in the liquid environment in which they existed. Then, according to some theories of cellular evolution, one of the early eukaryotic cells engulfed a prokaryote, and together the two cells formed a symbiotic relationship. In particular, the engulfed cell began to function as an organelle within the larger eukaryotic cell that consumed it. Both chloroplasts and mitochondria, which exist in modern eukaryotic cells and still retain their own genomes, are thought to have arisen in this manner. Of course, prokaryotic cells have continued to evolve as well. Different species of bacteria and archaea have adapted to specific environments, and these prokaryotes not only survive but thrive without having their genetic material in its own compartment. For example, certain bacterial species that live in thermal vents along the ocean floor can withstand higher temperatures than any other organisms on Earth. Origin of a eukaryotic cell. A prokaryotic host cell incorporates another prokaryotic cell. Each prokaryote has its own set of DNA molecules (a genome). The genome of the incorporated cell remains separate (curved blue line) from the host cell genome (curved purple line). 16 The incorporated cell may continue to replicate as it exists within the host cell. Over time, during errors of replication or perhaps when the incorporated cell lyses and loses its membrane separation from the host, genetic material becomes separated from the incorporated cell and merges with the host cell genome. Eventually, the host genome becomes a mixture of both genomes, and it ultimately becomes enclosed in an endomembrane, a membrane within the cell that creates a separate compartment. This compartment eventually evolves into a nucleus. Figure: The origin of mitochondria and chloroplasts Mitochondria and chloroplasts likely evolved from engulfed prokaryotes that once lived as independent organisms. At some point, a eukaryotic cell engulfed an aerobic prokaryote, which then formed an endosymbiotic relationship with the host eukaryote, gradually developing into a mitochondrion. Eukaryotic cells containing mitochondria then engulfed photosynthetic prokaryotes, which evolved to become specialized chloroplast. 1.2 Eukaryotic Cells Possess a Nucleus and Membrane-Bound Organelles How do cells accomplish all their functions in such a tiny, crowded package? Eukaryotic cells have evolved ways to partition off different functions to various locations in the cell. In fact, specialized compartments called organelles exist within eukaryotic cells for this purpose. Different organelles play different roles in the cell — for instance, mitochondria generate energy from food molecules; lysosomes break down and recycle organelles and macromolecules; and the endoplasmic reticulum helps build membranes and transport proteins throughout the cell. But what characteristics do all organelles have in common? And why was the development of three particular organelles (the nucleus, the mitochondrion, and the chloroplast) so essential to the evolution of present-day eukaryotes ? 17 What Defines an Organelle? In addition to the nucleus, eukaryotic cells may contain several other types of organelles, which may include mitochondria, chloroplasts, the endoplasmic reticulum, the Golgi apparatus, and lysosomes. Each of these organelles performs a specific function critical to the cell's survival. Moreover, nearly all eukaryotic organelles are separated from the rest of the cellular space by a membrane The membranes that surround eukaryotic organelles are based on lipid bilayers that are similar (but not identical) to the cell's outer membrane. Together, the total area of a cell's internal membranes far exceeds that of its plasma membrane. Like the plasma membrane, organelle membranes function to keep the inside "in" and the outside "out." This partitioning permits different kinds of biochemical reactions to take place in different organelles. Although each organelle performs a specific function in the cell, all of the cell's organelles work together in an integrated fashion to meet the overall needs of the cell. For example, biochemical reactions in a cell's mitochondria transfer energy from fatty acids and pyruvate molecules into an energy-rich molecule called adenosine triphosphate (ATP). Subsequently, the rest of the cell's organelles use this ATP as the source of the energy they need to operate. Because most organelles are surrounded by membranes, they are easy to visualize — with magnification. For instance, researchers can use high resolution electron microscopy to take a snapshot through a thin cross-section or slice of a cell. Other less powerful microscopy techniques coupled with organelle-specific stains have helped researchers see organelle structure more clearly, as well as the distribution of various organelles within cells. However, unlike the rooms in a house, a cell's organelles are not static. Rather, these structures are in constant motion, sometimes moving to a particular place within the cell, sometimes merging with other organelles, and sometimes growing larger or smaller. These dynamic changes in cellular structures can be observed with video microscopic techniques, which provide lower-resolution movies of whole organelles as these structures move within cells. The nucleus 18 Why Is the Nucleus So Important? Of all eukaryotic organelles, the nucleus is perhaps the most critical. In fact, the mere presence of a nucleus is considered one of the defining features of a eukaryotic cell. This structure is so important because it is the site at which the cell's DNA is housed and the process of interpreting it begins. Recall that DNA contains the information required to build cellular proteins. In eukaryotic cells, the membrane that surrounds the nucleus (nuclear envelope) partitions this DNA from the cell's protein synthesis machinery, which is located in the cytoplasm. Tiny pores in the nuclear envelope, called nuclear pores, then selectively permit certain macromolecules to enter and leave the nucleus — including the RNA molecules that carry information from a cellular DNA to protein manufacturing centers in the cytoplasm. This separation of the DNA from the protein synthesis machinery provides eukaryotic cells with more intricate regulatory control over the production of proteins and their RNA intermediates. In contrast, the DNA of prokaryotic cells is distributed loosely around the cytoplasm, along with the protein synthesis machinery. This closeness allows prokaryotic cells to rapidly respond to environmental change by quickly altering the types and amount of proteins they manufacture. Mitochondria and Chloroplasts Why Are Mitochondria and Chloroplasts Special? 19 These specialized structures are enclosed by double membranes, and they are believed to have originated back when all living things on Earth were single-celled organisms. At that time, some larger eukaryotic cells with flexible membranes "ate" by engulfing molecules and smaller cells — and scientists believe that mitochondria and chloroplasts arose as a result of this process. In particular, researchers think that some of these "eater" eukaryotes engulfed smaller prokaryotes, and a symbiotic relationship subsequently developed. Once kidnapped, the "eaten" prokaryotes continued to generate energy and carry out other necessary cellular functions, and the host eukaryotes came to rely on the contribution of the "eaten" cells. Over many generations, the descendants of the eukaryotes developed mechanisms to further support this system, and concurrently, the descendants of the engulfed prokaryotes lost the ability to survive on their own, evolving into present-day mitochondria and chloroplasts. This proposed origin of mitochondria and chloroplasts is known as the endosymbiotic hypothesis. These specialized structures are enclosed by double membranes, and they are believed to have originated back when all living things on Earth were single- celled organisms. At that time, some larger eukaryotic cells with flexible membranes "ate" by engulfing molecules and smaller cells — and scientists believe that mitochondria and chloroplasts arose as a result of this process. In particular, researchers think that some of these "eater" eukaryotes engulfed smaller prokaryotes, and a symbiotic relationship subsequently developed. Once kidnapped, the "eaten" prokaryotes continued to generate energy and carry out other necessary cellular functions, and the host eukaryotes came to rely on the contribution of the "eaten" cells. Over many generations, the descendants of the eukaryotes developed mechanisms to further support this system, and concurrently, the descendants of the engulfed prokaryotes lost the ability to survive on their own, evolving into present-day mitochondria and chloroplasts. This proposed origin of mitochondria and chloroplasts is known as the endosymbiotic hypothesis. In addition to double membranes, mitochondria and chloroplasts also retain small genomes with some resemblance to those found in modern prokaryotes. This finding provides yet additional evidence that these organelles probably originated as self- sufficient single-celled organisms. 20 Today, mitochondria are found in fungi, plants, and animals, and they use oxygen to produce energy in the form of ATP molecules, which cells then employ to drive many processes. Scientists believe that mitochondria evolved from aerobic, or oxygen- consuming, prokaryotes. In comparison, chloroplasts are found in plant cells and some algae, and they convert solar energy into energy-storing sugars such as glucose. Chloroplasts also produce oxygen, which makes them necessary for all life as we know it. Scientists think chloroplasts evolved from photosynthetic prokaryotes similar to modern- day cyanobacteria. 21 Figure: Typical prokaryotic (left) and eukaryotic (right) cells In prokaryotes, the DNA (chromosome) is in contact with the cellular cytoplasm and is not in a housed membrane-bound nucleus. In eukaryotes, however, the DNA takes the form of compact chromosomes separated from the rest of the cell by a nuclear membrane (also called a nuclear envelope). Eukaryotic cells also contain a variety of structures and organelles not present in prokaryotic cells. Throughout the course of evolution, organelles such as mitochondria and chloroplasts (a form of plastid) may have arisen from engulfed prokaryotes. © 1998 Nature Publishing Group Doolittle, W. F. A paradigm gets shifty. Nature 392, 15-16 (1998). All rights reserved. 22 1.3 Cell Function Depends on the Continual Uptake and Conversion of Energy How Do Eukaryotic Cells Handle Energy? Mitochondria enable eukaryotes to make more efficient use of food sources than their prokaryotic counterparts. That's because these organelles greatly expand the amount of membrane used for energy-generating electron transport chains. In addition, mitochondria use a process called oxidative metabolism to convert food into energy, and oxidative metabolism yields more energy per food molecule than non-oxygen-using, or anaerobic, methods. Energywise, cells with mitochondria can therefore afford to be bigger than cells without mitochondria.Within eukaryotic cells, mitochondria function somewhat like batteries, because they convert energy from one form to another: food nutrients to ATP. Accordingly, cells with high metabolic needs can meet their higher energy demands by increasing the number of mitochondria they contain. For example, muscle cells in people who exercise regularly possess more mitochondria than muscle cells in sedentary people. Prokaryotes, on the other hand, don't have mitochondria for energy production, so they must rely on their immediate environment to obtain usable energy. Prokaryotes generally use electron transport chains in their plasma membranes to provide much of their energy. The actual energy donors and acceptors for these electron transport chains are quite variable, reflecting the diverse range of habitats where prokaryotes live. (In aerobic prokaryotes, electrons are transferred to oxygen, much as in the mitochondria.) The challenges associated with energy generation limit the size of prokaryotes. As these cells grow larger in volume, their energy needs increase proportionally. However, as they increase in size, their surface area (and thus their 23 ability to both take in nutrients and transport electron) does not increase to the same degree as their volume. As a result, prokaryotic cells tend to be small so that they can effectively manage the balancing act between energy supply and demand. Figure: The relationship between the radius, surface area, and volume of a cell. Note that as the radius of a cell increases from 1x to 3x (left), the surface area increases from 1x to 9x, and the volume increases from 1x to 27x. Where Do Cells Obtain Their Energy? Cells, like humans, cannot generate energy without locating a source in their environment. However, whereas humans search for substances like fossil fuels to power their homes and businesses, cells seek their energy in the form of food molecules or sunlight. In fact, the Sun is the ultimate source of energy for almost all cells, because photosynthetic prokaryotes, algae, and plant cells harness solar energy and use it to make the complex organic food molecules that other cells rely on for the energy required to sustain growth, metabolism, and reproduction. Cellular nutrients come in many forms, including sugars and fats. In order to provide a cell with energy, these molecules have to pass across the cell membrane, which functions as a barrier — but not an impassable one. Like the exterior walls of a house, the plasma membrane is semi-permeable. In much the same way that doors and windows allow necessities to enter the house, various proteins that span the cell membrane permit specific molecules into the cell, although they may require some energy input to accomplish this task. Cells can incorporate nutrients by phagocytosis. This amoeba, a single-celled organism, acquires energy by engulfing nutrients in the form of a yeast cell (red). Through a process called phagocytosis, the amoeba encloses the yeast cell with its 24 membrane and draws it inside. Specialized plasma membrane proteins in the amoeba (in green) are involved in this act of phagocytosis, and they are later recycled back into the amoeba after the nutrients are engulfed. How Do Cells Turn Nutrients into Usable Energy? cells release the energy stored in their food molecules through a series of oxidation reactions. Oxidation describes a type of chemical reaction in which electrons are transferred from one molecule to another, changing the composition and energy content of both the donor and acceptor molecules. Food molecules act as electron donors. During each oxidation reaction involved in food breakdown, the product of the reaction has a lower energy content than the donor molecule that preceded it in the pathway. At the same time, electron acceptor molecules capture some of the energy lost from the food molecule during each oxidation reaction and store it for later use. Eventually, when the carbon atoms from a complex organic food molecule are fully oxidized at the end of the reaction chain, they are released as waste in the form of carbon dioxide. Figure: The release of energy from sugar 25 Compare the stepwise oxidation (left) with the direct burning of sugar (right). Through a series of small steps, free energy is released from sugar and stored in carrier molecules in the cell (ATP and NADH, not shown). On the right, the direct burning of sugar requires a larger activation energy. In this reaction, the same total free energy is released as in stepwise oxidation, but none is stored in carrier molecules, so most of it will be lost as heat (free energy). This direct burning is therefore very inefficient, as it does not harness energy for later use. Cells do not use the energy from oxidation reactions as soon as it is released. Instead, they convert it into small, energy-rich molecules such as ATP and nicotinamide adenine dinucleotide (NADH), which can be used throughout the cell to power metabolism and construct new cellular components. In addition, workhorse proteins called enzymes use this chemical energy to catalyze, or accelerate, chemical reactions within the cell that would otherwise proceed very slowly. Enzymes do not force a reaction to proceed if it wouldn't do so without the catalyst; rather, they simply lower the energy barrier required for the reaction to begin. Figure: Enzymes allow activation energies to be lowered. Enzymes lower the activation energy necessary to transform a reactant into a product. On the left is a reaction that is not catalyzed by an enzyme (red), and on the right is one that is (green). In the enzyme- catalyzed reaction, an enzyme will bind to a reactant and facilitate its transformation into a product. Consequently, an enzyme-catalyzed reaction pathway has a smaller energy barrier (activation energy) to overcome before the reaction can proceed. What Specific Pathways Do Cells Use? The particular energy pathway that a cell employs depends in large part on whether that cell is a eukaryote or a prokaryote. Eukaryotic cells use three major processes to transform the energy held in the chemical bonds of food molecules into more readily usable forms — often energy- rich carrier molecules. 26 Adenosine 5'-triphosphate, or ATP, is the most abundant energy carrier molecule in cells. This molecule is made of a nitrogen base (adenine), a ribose sugar, and three phosphate groups. The word adenosine refers to the adenine plus the ribose sugar. The bond between the second and third phosphates is a high-energy bond. Figure: An ATP molecule ATP consists of an adenosine base (blue), a ribose sugar (pink) and a phosphate chain. The high-energy phosphate bond in this phosphate chain is the key to ATP's energy storage potential. 27  1- glycolysis The first process in the eukaryotic energy pathway is glycolysis, which literally means "sugar splitting." During glycolysis, single molecules of glucose are split and ultimately converted into two molecules of a substance called pyruvate; because each glucose contains six carbon atoms, each resulting pyruvate contains just three carbons. Glycolysis is actually a series of ten chemical reactions that requires the input of two ATP molecules. This input is used to generate four new ATP molecules, which means that glycolysis results in a net gain of two ATPs. Two NADH molecules are also produced; these molecules serve as electron carriers for other biochemical reactions in the cell. Glycolysis is an ancient, major ATP-producing pathway that occurs in almost all cells, eukaryotes and prokaryotes alike. This process, which is also known as fermentation, takes place in the cytoplasm and does not require oxygen. However, the fate of the pyruvate produced during glycolysis depends upon whether oxygen is present. In the absence of oxygen, the pyruvate cannot be completely oxidized to carbon dioxide, so various intermediate products result. For example, when oxygen levels are low, skeletal muscle cells rely on glycolysis to meet their intense energy requirements. This reliance on glycolysis results in the buildup of an intermediate known as lactic acid, which can cause a person's muscles to feel as if they are "on fire." Similarly, yeast, which is a single-celled eukaryote, produces alcohol (instead of carbon dioxide) in oxygen-deficient settings. 2- Cetric acid cycle when oxygen is available, the pyruvates produced by glycolysis become the input for the next portion of the eukaryotic energy pathway. During this stage, each pyruvate molecule in the cytoplasm enters the mitochondrion, where it is converted into acetyl CoA, a two-carbon energy carrier, and its third carbon combines with oxygen and is released as carbon dioxide. At the same time, an NADH carrier is also generated. Acetyl CoA then enters a pathway called the citric acid cycle, which is the second major energy process used by cells. The eight-step citric acid cycle generates: a. three more NADH molecules and b. two other carrier molecules: FADH2 and GTP. 28  3- Electron transport chain The third major process in the eukaryotic energy pathway involves an electron transport chain, catalyzed by several protein complexes located in the mitochondrional inner membrane. This process, called oxidative phosphorylation, transfers electrons from NADH and FADH2 through the membrane protein complexes, and ultimately to oxygen, where they combine to form water. As electrons travel through the protein complexes in the chain, a gradient of hydrogen ions, or protons, forms across the mitochondrial membrane. Cells harness the energy of this proton gradient to create three additional ATP molecules for every electron that travels along the chain. Overall, the combination of the citric acid cycle and oxidative phosphorylation yields much more energy than fermentation - 15 times as much energy per glucose molecule! Together, these processes that occur inside the mitochondion, the citric acid cycle and oxidative phosphorylation, are referred to as respiration, a term used for processes that couple the uptake of oxygen and the production of carbon dioxide. The electron transport chain in the mitochondrial membrane is not the only one that generates energy in living cells. In plant and other photosynthetic cells, chloroplasts also have an electron transport chain that harvests solar energy. Even though they do not contain mitochondria or chloroplasts, prokaryotes have other kinds of energy- yielding electron transport chains within their plasma membranes that also generate energy. 29 1-4 Photosynthetic Cells Capture Light Energy and Convert It to Chemical Energy Cells get nutrients from their environment, but where do those nutrients come from? Virtually all organic material on Earth has been produced by cells that convert energy from the Sun into energy-containing macromolecules. This process, called photosynthesis, is essential to the global carbon cycle and organisms that conduct photosynthesis represent the lowest level in most food chains. What Is Photosynthesis? Why Is it Important? Cells use carbon dioxide and energy from the Sun to make sugar molecules and oxygen. These sugar molecules are the basis for more complex molecules made by the photosynthetic cell, such as glucose. Then, via respiration processes, cells use oxygen and glucose to synthesize energy- rich carrier molecules, such as ATP, and carbon dioxide is produced as a waste product. Therefore, the synthesis of glucose and its breakdown by cells are opposing processes. Photosynthesis doesn't just drive the carbon cycle — it also creates the oxygen necessary for respiring organisms. Although green plants contribute much of the 30 oxygen in the air we breathe, phytoplankton and cyanobacteria in the world's oceans are thought to produce between one-third and one-half of atmospheric oxygen on Earth. Photosynthetic cells contain special pigments that absorb light energy. Different pigments respond to different wavelengths of visible light. Chlorophyll, the primary pigment used in photosynthesis, reflects green light and absorbs red and blue light most strongly. In plants, photosynthesis takes place in chloroplasts, which contain the chlorophyll. Structure: Chloroplasts are surrounded by a double membrane and contain a third inner membrane, called the thylakoid membrane, that forms long folds within the organelle. In electron micrographs, thylakoid membranes look like stacks of coins, although the compartments they form are connected like a maze of chambers. The green pigment chlorophyll is located within the thylakoid membrane, and the space between the thylakoid and the chloroplast membranes is called the stroma. Chlorophyll A is the major pigment used in photosynthesis, but there are several types of chlorophyll and numerous other pigments that respond to light, including red, brown, and blue pigments. These other pigments may help channel light energy to chlorophyll A or protect the cell from photo-damage. For example, the photosynthetic protists called dinoflagellates, which are responsible for the "red tides" that often prompt warnings against eating shellfish, contain a variety of light-sensitive pigments, including both chlorophyll and the red pigments responsible for their coloration. 31 What Are the Steps of Photosynthesis? Photosynthesis consists of both light-dependent reactions and light-independent reactions. The so-called "light" reactions occur within the chloroplast thylakoids, where the chlorophyll pigments reside. When light energy reaches the pigment molecules, it energizes the electrons within them, and these electrons are shunted to an electron transport chain in the thylakoid membrane. Every step in the electron transport chain then brings each electron to a lower energy state and harnesses its energy by producing ATP and NADPH. Meanwhile, each chlorophyll molecule replaces its lost electron with an electron from water; this process essentially splits water molecules to produce oxygen. 32 Once the light reactions have occurred, the light-independent or "dark" reactions take place in the chloroplast stroma. During this process, also known as carbon fixation, energy from the ATP and NADPH molecules generated by the light reactions drives a chemical pathway that uses the carbon in carbon dioxide to build a three-carbon sugar called glyceraldehyde-3-phosphate (G3P). Cells then use G3P to build a wide variety of other sugars (such as glucose) and organic molecules. Many of these interconversions occur outside the chloroplast, following the transport of G3P from the stroma. The products of these reactions are then transported to other parts of the cell, including the mitochondria, where they are broken down to make more energy carrier molecules to satisfy the metabolic demands of the cell. In plants, some sugar molecules are stored as sucrose or starch. 1.5 Metabolism is the Complete Set of Biochemical Reactions within a Cell A cell's daily operations are accomplished through the biochemical reactions that take place within the cell. Reactions are turned on and off or sped up and slowed down according to the cell's immediate needs and overall functions. At any given time, the numerous pathways involved in building up and breaking down cellular components must be monitored and balanced in a coordinated fashion. To achieve this goal, cells organize reactions into various enzyme-powered pathways. What Do Enzymes Do? Enzymes are protein catalysts that speed biochemical reactions by facilitating the molecular rearrangements that support cell function. Recall that chemical reactions convert substrates into products, often by attaching chemical groups to or breaking off chemical groups from the substrates. Enzymes are flexible proteins that change shape when they bind with substrate molecules. In fact, this binding and shape changing ability is how enzymes manage to increase reaction rates. 33