Plant Cell Biology Notes PDF

Botany Department Faculty of Science Port Said University Plant Cell Biology Prepared By/ Dr. Raghda Hassan Shahda 2025 1  Cell Biolo...

Botany Department Faculty of Science Port Said University Plant Cell Biology Prepared By/ Dr. Raghda Hassan Shahda 2025 1  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 19 Why Are Mitochondria and Chloroplasts Special? 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 20 provides yet additional evidence that these organelles probably originated as self- sufficient single-celled organisms. 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. 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. 21 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 22 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 23 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 24 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. 25 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. 26  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. 27  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. 28 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 29 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. 30 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. 31 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. 32 In many cases, enzymes function by bringing two substrates into close proximity and orienting them for easier electron transfer. Shape or conformational changes can also act as an on/off switch. For example, when inhibitor molecules bind to a site on an enzyme distinct from the substrate site, they can make the enzyme assume an inactive conformation, thereby preventing it from catalyzing a reaction. Conversely, the binding of activator molecules can make an enzyme assume an active conformation, essentially turning it on. What Are Metabolic Pathways? Many of the molecular transformations that occur within cells require multiple steps to accomplish. e.g., Cells split one glucose molecule into two pyruvate molecules by way of a ten- step process called glycolysis. This coordinated series of chemical reactions is an example of a metabolic pathway in which the product of one reaction becomes the substrate for the next reaction. Consequently, the intermediate products of a metabolic pathway may be short-lived. Enzymes can be involved at every step in a reaction pathway. 33 How Do Cells Keep Chemical Reactions in Balance? Cells are expert recyclers. They disassemble large molecules into simpler building blocks and then use those building blocks to create the new components they require. The breaking down of complex organic molecules occurs via catabolic pathways and usually involves the release of energy. Through catabolic pathways, polymers such as proteins, nucleic acids, and polysaccharides are reduced to their constituent parts: amino acids, nucleotides, and sugars, respectively. In contrast, the synthesis of new macromolecules occurs via anabolic pathways that require energy input. Cells must balance their catabolic and anabolic pathways in order to control their levels of critical metabolites (those molecules created by enzymatic activity ) and ensure that sufficient energy is available. For example, if supplies of glucose start to wane, as might happen in the case of starvation, cells will synthesize glucose from other materials or start sending fatty acids into the citric acid cycle to generate ATP. Conversely, in times of plenty, excess glucose is converted into storage forms, such as glycogen, starches, and fats. 34 Not only do cells need to balance catabolic and anabolic pathways, but they must also monitor the needs and surpluses of all their different metabolic pathways. In order to bolster a particular pathway, cells can increase the amount of a necessary (rate-limiting) enzyme or use activators to convert that enzyme into an active conformation. Conversely, to slow down or halt a pathway, cells can decrease the amount of an enzyme or use inhibitors to make the enzyme inactive. Such up- and down-regulation of metabolic pathways is often a response to changes in concentrations of key metabolites in the cell. For example, a cell may take stock of its levels of intermediate metabolites and tune the glycolytic pathway and the synthesis of glucose accordingly. In some instances, the products of a metabolic pathway actually serve as inhibitors of their own synthesis, in a process known as feedback inhibition. For example, the first intermediate in glycolysis, glucose- 6-phosphate, inhibits the very enzyme that produces it, hexokinase. Feedback inhibition When there is enough product at the end of a reaction pathway (red macromolecule), it can inhibit its own synthesis by interacting with enzymes in the synthesis pathway (red arrow). 35  Vacuoles Vacuoles vary in shape and size in relation to the stage of development and the metabolic state of the cell. In meristematic cells, vacuoles are often very small and numerous. In mature cells, There is usually one large vacuole occupying the central part of the protoplast, whereas the cytoplasm and other protoplasmic components are restricted to a parietal position. ERGASTIC SUBSTANCES These are the products of metabolism and represented by reserve or waste products. They include: the visible carbohydrates, cellulose and starch, protein bodies, fats and related substances, mineral matter in the form of crystals. Among the ergastic substances are secondary products, which are not of great importance in plant metabolism. Many of these compounds are not produced by all plants and some by very few. However, these compounds are usually of considerable importance to man as sources of drugs and other purposes. These include tannins, resins, gums, rubber, flavonoids and alkaloids. 36   Carbohydrates These are the most abundant organic compounds of life, such as glucose and fructose. When two monosaccharides combine to form disaccharides, e.g., sucrose. Polysaccharides are formed from the combination of more than two monosaccharides. The principal polysaccharides in the plants are cellulose and starch. Pectic compounds are carbohydrates which often found in association with cellulose and form the primary cementing substances between cell walls. Lignin is also found in conjunction with cellulose in secondary cell walls. It is a very complicated, highly branched polymer that gives rigidity and causes the wood to resist decomposers. How are starch grains formed? Starch grains show obvious concentric layering. The deposition of starch occurs around a point called the hilum. This is referred to:  The difference in density and water content in the different successive layers  Alternating two different types of starch e.g. amylose and amylopectin. 37  Type of layering depending on the location of the hilum. Excentric Concentric layering layering Type of layering depending on the location of the hilum. Excentric Concentric layering layering 38   Proteins Proteins are the main ingredients of the living protoplasmic bodies, but they also occur as inactive ergastic substances. Ergastic protein occurs in the cell as a reserve material in amorphous or crystal-like form. In many seeds, there are special type of protein grains known as the Aleurone grains, e.g., in the seeds of castor oil plant (Ricinus conumunis). Each aleurone grain is enclosed within a membrane and contains inclusions of globoids and crystalloids of protein, which are embedded in simple proteins. One or more globoid or crystalloid is present in the aleurone grain.  Crystals Crystals are the end products of the metabolic processes of the cell. These crystals are of differing chemical composition and are found in many kinds of cells and plants. The inorganic deposits in plants consist mostly of calcium salts and of anhydrides of silica. 39  CALCIUM Calcium Calcium oxalates carbonate Solita raphi druse Cysto 40  3-THE CELL CYCLE & MITOSIS A human, as well as every sexually reproducing organism, begins life as a fertilized egg or zygote. Trillions of cell divisions subsequently occur in a controlled manner to produce a complex, multicellular human. Single-celled organisms use cell division as their method of reproduction. 1.1 DNA Organization and the Cell Cycle The cell cycle is an orderly sequence of events that describes the stages of a cell’s life from the division of a single parent cell to the production of two genetically identical new daughter cells. The mechanisms involved in the cell cycle are highly regulated. 1.1.1 Genomic DNA Before discussing the steps a cell must undertake to replicate, we need a deeper understanding of the structure and function of a cell’s genetic information. A cell’s DNA, packaged as double-stranded DNA molecules, is called its genome. In prokaryotes, the genome is composed of a single circular double-stranded DNA molecule. The region in the cell containing this genetic material is called a nucleoid. Some prokaryotes also have smaller loops of non- essential DNA called plasmids. Bacteria can exchange these plasmids with other bacteria, sometimes receiving beneficial new genes that the recipient can add to their chromosomal DNA. Antibiotic resistance is one trait that often spreads through a bacterial colony through plasmid exchange. In eukaryotic cells, the genome consists of several double-stranded linear DNA molecules. Each species has a characteristic number of chromosomes in the nuclei of its cells. Human body cells have 46 chromosomes, while human gametes (sperm or eggs) have 23 chromosomes each. A typical body cell, or somatic cell, contains two matched sets of chromosomes, a configuration known as diploid. The letter n is used to represent a single set of chromosomes; therefore, a diploid organism is designated 2n. 41 Human cells that contain one set of chromosomes are called gametes, or sex cells; these are eggs and sperm, and are designated 1n, or haploid. Matched pairs of chromosomes in a diploid organism are called homologous (“same knowledge”) chromosomes. Homologous chromosomes are the same length and have specific nucleotide segments called genes in exactly the same location, or locus. Genes are the functional units of chromosomes and determine specific characteristics by coding for specific proteins. Traits are the variations of those characteristics. For example, hair color is a characteristic with traits that are blonde, brown, or black. Each copy of a homologous pair of chromosomes originates from a different parent; therefore, the genes themselves are not identical. The variation of individuals within a species is due to the specific combination of the genes inherited from both parents. Even a slightly altered sequence of nucleotides within a gene can result in an alternative trait. A karyotype of human chromosomes, showing their distinct sizes and banding patterns. In this image, the chromosomes were exposed to fluorescent stains to highlight chromosomes in different colors. 42  1.1.2 Eukaryotic Chromosomal Structure and Compaction If the DNA from all 46 chromosomes in a human cell nucleus was laid out end to end, it would measure approximately two meters; however, its diameter would be only 2 nm. Considering that the size of a typical human cell is about 10 µm (100,000 cells lined up to equal one meter), DNA must be tightly packaged to fit in the cell’s nucleus. At the same time, it must also be readily accessible for the genes to be expressed. During some stages of the cell cycle, the long strands of DNA are condensed into compact chromosomes. There are a number of ways that chromosomes are compacted. 43 DNA replicates in the S phase of interphase. After replication, the chromosomes are composed of two linked sister chromatids. When fully compact, the pairs of identically packed chromosomes are bound to each other by cohesin proteins. The connection between the sister chromatids is closest in a region called the centromere. The conjoined sister chromatids, with a diameter of about 1 µm, are visible under a light microscope. The centromeric region is highly condensed and thus will appear as a constricted area. 44  1.2 | The Cell Cycle The cell cycle is an ordered series of events involving cell growth and cell division that produces two new daughter cells. Somatic cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages of growth, DNA replication, and division that produces two genetically identical cells. In other words, a typical 2n somatic cell will divide into two 2n somatic cells that are genetically identical. This is a form of asexual reproduction. we see two major phases: interphase and the M phase. During interphase, the cell undergoes three distinct periods: G1, S, and G2. During G1, S, and G2, the cell grows, DNA is replicated, and the cell grows some more. During the M phase, the cell undergoes two distinct periods: mitosis (also called karyokinesis) and cytokinesis, the division of the cytoplasm. Figure: cell cycle 45 1.2.1 Interphase During interphase, the cell undergoes normal growth processes while also preparing for cell division. In order for a cell to move from interphase into the mitotic phase, many internal and external conditions must be met. The three aspects or stages of interphase are called G1, S, and G2. G1 Phase (First Gap) The first stage of interphase is called the G1 phase (first gap) because, from a microscopic aspect, little change is visible. However, during the G1 stage, the cell is quite active at the biochemical level. The cell is accumulating the building blocks of chromosomal DNA and the associated proteins as well as accumulating sufficient energy reserves to complete the task of replicating each chromosome in the nucleus. S Phase (Synthesis of DNA) Throughout interphase, nuclear DNA remains in a semi-condensed chromatin configuration. In the S phase, DNA replication can proceed to form identical pairs of DNA molecules—sister chromatids—that are firmly attached to the centromeric region. The centrosome is duplicated during the S phase. The two centrosomes will give rise to the mitotic spindle, the apparatus that orchestrates the movement of chromosomes during mitosis. At the center of each animal cell, the centrosomes of animal cells are associated with a pair of rod-like objects, the centrioles, which are at right angles to each other. Centrioles help organize cell division. Centrioles are not present in the centrosomes of other eukaryotic species, such as plants and most fungi. G2 Phase (Second Gap) In the G2 phase, the cell replenishes its energy stores and synthesizes proteins necessary for chromosome manipulation. Some cell organelles are duplicated, and the cytoskeleton is dismantled to provide resources for the mitotic phase. There may be additional cell growth during G2. The final preparations for the mitotic phase must be completed before the cell is able to enter the first stage of mitosis. 46  1.2.2 The Mitotic Phase The mitotic phase is a multistep process during which the duplicated chromosomes are aligned, separated, and moved into two new, identical daughter cells. M phase is divided into mitosis and cytokinesis. Mitosis Mitosis is divided into a series of phases—Prophase, Prometaphase, Metaphase, Anaphase, and Telophase—that result in the division of the cell nucleus. 47 48 Cytokinesis Cytokinesis, or “cell motion,” is the second main stage of the mitotic phase during which cell division is completed via the physical separation of the cytoplasmic components into two daughter cells. Division is not complete until the cell components have been apportioned and completely separated into the two daughter cells. Although the stages of mitosis are similar for most eukaryotes, the process of cytokinesis is quite different for eukaryotes that have cell walls, such as plant cells. In cells such as animal cells that lack cell walls, cytokinesis actually begins at the midpoint of Anaphase. A contractile ring composed of actin filaments forms just inside the plasma membrane at the former Metaphase plate. The actin filaments pull the equator of the cell inward, forming a constriction. This constriction or fissure is called the cleavage furrow. The furrow deepens as the actin ring contracts, and eventually the membrane is cleaved in two. In plant cells, a new cell wall must form between the daughter cells. During interphase, the Golgi apparatus accumulates enzymes, structural proteins, and glucose molecules prior to breaking into vesicles and dispersing throughout the dividing cell. During telophase, these Golgi vesicles are transported on microtubules to form a phragmoplast (a vesicular structure) at the metaphase plate. There, the vesicles fuse and coalesce from the center toward the cell walls; this structure is called a cell plate. As more vesicles fuse, the cell plate enlarges until it merges with the cell walls at the periphery of the cell. Enzymes use the glucose that has accumulated between the membrane layers to build a new cell wall made of cellulose. Remember that cellulose is a structural polymer of glucose. The Golgi membranes become parts of the plasma membrane on either side of the new cell wall. 49  1.2.3 G0 Phase (A variation of the cell cycle) Not all cells adhere to the classic cell cycle pattern in which a newly formed daughter cell immediately enters the preparatory phases of interphase, closely followed by the mitotic phase. Cells in G0 phase (“G zero”) are not actively preparing to divide. The cell is in a quiescent (inactive) stage that occurs when cells exit the cell cycle. Some cells enter G0 temporarily until an external signal triggers the onset of G1. Other cells that never or rarely divide, such as mature cardiac muscle and nerve cells, remain in G0 permanently. Although cells in G0 are inactive in the sense that they are not actively preparing for and undergoing cell division, they can be very active in other ways. Many cells in the adult body for instance, are permanently in G0 while fulfilling their specialized functions. 50  1.3.2 Regulation of the Cell Cycle at Internal Checkpoints It is essential that the daughter cells that have been produced be exact duplicates of the parent cell. Mistakes in the duplication or distribution of the chromosomes lead to mutations that may be passed forward to every new cell produced from an abnormal cell. To prevent a compromised cell from continuing to divide, there are internal control mechanisms that operate at three main cell cycle checkpoints. A checkpoint is one of several points in the eukaryotic cell cycle at which the progression of a cell to the next stage in the cycle can be halted until conditions are favorable. These checkpoints occur: 1. near the end of G1, 2. at the G2/M transition, and 3. during metaphase. 1- The G1 Checkpoint The G1 checkpoint determines whether all conditions are favorable for cell division to proceed. The G1 checkpoint, also called the restriction point (in yeast), is a point at which the cell irreversibly commits to the cell division process. External influences, such as growth factors, play a large role in carrying the cell past the G1 checkpoint. In addition to adequate reserves and cell size, there is a check for genomic DNA damage at the G1 checkpoint. A cell that does not meet all the requirements will not be allowed to progress into the S phase. The cell can halt the cycle and attempt to remedy the problematic condition, or the cell can advance into G0 and await further signals when conditions improve. 2- The G2 Checkpoint The G2 checkpoint bars entry into the mitotic phase if certain conditions are not met. 51  As at the G1 checkpoint, cell size and protein reserves are assessed. However, the most important role of the G2 checkpoint is to ensure that all of the chromosomes have been replicated and that the replicated DNA is not damaged. If the checkpoint mechanisms detect problems with the DNA, the cell cycle is halted, and the cell attempts to either complete DNA replication or repair the damaged DNA. 3- The M Checkpoint The M checkpoint occurs near the end of the metaphase stage of mitosis. The M checkpoint is also known as the spindle checkpoint, because it determines whether all of the sister chromatids are correctly attached to the spindle microtubules. Because the separation of the sister chromatids during anaphase is an irreversible step, the cycle will not proceed until the kinetochores of each pair of sister chromatids are firmly anchored to at least two spindle fibers arising from opposite poles of the cell. 52 Unit 4. The Endoplasmic Reticulum, Golgi Apparatus, and Lysosomes Are Part of an Extensive Endomembrane System in Eukaryotic Cells Cells have extensive sets of intracellular membranes, which together compose the endomembrane system. The endomembrane system was first discovered in the late 1800s when scientist Camillo Golgi noticed that a certain stain selectively marked only some internal cellular membranes. Golgi thought that these intracellular membranes were interconnected, but advances in microscopy and biochemical studies of the various membrane-encased organelles later made it clear the organelles in the endomembrane system are separate compartments with specific functions. These structures do exchange membrane material, however, via a special type of transport. Today, scientists know that the endomembrane system includes the endoplasmic reticulum (ER), Golgi apparatus, and lysosomes. Vesicles also allow the exchange of membrane components with a cell's plasma membrane. How Are Cell Membranes Synthesized? Membranes and their constituent proteins are assembled in the ER. This organelle contains the enzymes involved in lipid synthesis, and as lipids are manufactured in the ER, they are inserted into the organelle's own membranes. This happens in part because the lipids are too hydrophobic to dissolve into the cytoplasm. Similarly, transmembrane proteins have enough hydrophobic surfaces that they are also inserted into the ER membrane while they are still being synthesized. Here, future membrane proteins make their way to the ER membrane with the help of a signal sequence in the newly translated protein. The signal sequence stops translation and directs the ribosomes — which are carrying the unfinished proteins — to dock with ER proteins before finishing their work. Translation then recommences after the signal sequence docks with the ER, and it takes place within the ER membrane. Thus, by the time the protein achieves its final form, it is already inserted into a membrane. 53 Figure:A signal sequence on a growing protein will bind with a signal recognition particle (SRP). This slows protein synthesis. The SRP then binds to a location on the surface of the nearby ER. Then, the SRP is released, and the protein-ribosome complex is at the correct location for movement of the protein through a translocation channel. The proteins that will be secreted by a cell are also directed to the ER during translation, where they end up in the lumen, the internal cavity, where they are then packaged for vesicular release from the cell. The hormones insulin and erythropoietin (EPO) are both examples of vesicular proteins. 54 How Are Organelle Membranes Maintained? The ER, Golgi apparatus, and lysosomes are not continuous with one another. Therefore, the membrane lipids and proteins that are synthesized in the ER must be transported through the network to their final destination in membrane- bound vesicles. Cargo-bearing vesicles pinch off of one set of membranes and travel along microtubule tracks to the next set of membranes, where they fuse with these structures. Trafficking occurs in both directions; the forward direction takes vesicles from the site of synthesis to the Golgi apparatus and next to a cell's lysosomes or plasma membrane. Vesicles that have released their cargo return via the reverse direction. The proteins that are synthesized in the ER have a signal that directs them where to go, much like an address directs a letter to its destination. Soluble proteins are carried in the lumens of vesicles. Any proteins that are destined for a lysosome are delivered to the lysosome interior when the vesicle that carries them fuses with the lysosomal membrane and joins its contents. In contrast, the proteins that will be secreted by a cell, such as insulin and EPO, are held in storage vesicles. When signaled by the cell, these vesicles fuse with the plasma membrane and release their contents into the extracellular space. What Does the Golgi Apparatus Do? Function The Golgi apparatus functions as a molecular assembly line in which membrane proteins undergo extensive post-translational modification. Many Golgi reactions involve the addition of sugar residues to membrane proteins and secreted proteins. The carbohydrates that the Golgi attaches to membrane proteins are often quite complex, and their synthesis requires multiple steps. Structure: In electron micrographs, the Golgi apparatus looks like a set of flattened sacs. Proteins enter the Golgi on the side facing the ER (cis side), and exit on the opposite side of the stack, facing the plasma membrane of the cell (trans side). Vesicles that bud off from the ER fuse with the closest Golgi membranes, called the cis-Golgi. Molecules then travel through the Golgi apparatus via vesicle transport until they reach the end of the assembly line at the farthest sacs from the ER — called the trans-Golgi. 55 At each workstation along the assembly line, Golgi enzymes catalyze distinct reactions. Later, as vesicles of membrane lipids and proteins bud off from the trans- Golgi, they are directed to their appropriate destinations — either lysosomes, storage vesicles, or the plasma membrane Membrane transport into and out of the cell Transport of molecules within a cell and out of the cell requires a complex endomembrane system. Endocytosis occurs when the cell membrane engulfs particles (dark blue) outside the cell, draws the contents in, and forms an intracellular vesicle called an endosome. This vesicle travels through the cell, and its contents are digested as it merges with vesicles containing enzymes from the Golgi. The vesicle is then known as a lysosome when its contents have been digested by the cell. Exocystosis is the process of membrane transport that releases cellular contents outside of the cell. Here, a transport vesicle from the Golgi or elsewhere in the cell merges its membrane with the plasma membrane and releases its contents. In this way, membranes are continually recycled and reused for different purposes throughout the cell. Membrane transport also occurs between the endoplasmic reticulum and the Golgi. 56 What Do Lysosomes Do? Lysosomes break down macromolecules into their constituent parts, which are then recycled. These membrane-bound organelles contain a variety of enzymes called hydrolases that can digest proteins, nucleic acids, lipids, and complex sugars. The lumen of a lysosome is more acidic than the cytoplasm. This environment activates the hydrolases and confines their destructive work to the lysosome. In plants and fungi, lysosomes are called acidic vacuoles. Lysosomes are formed by the fusion of vesicles that have budded off from the trans- Golgi. The sorting system recognizes address sequences in the hydrolytic enzymes and directs them to growing lysosomes. In addition, vesicles that bud off from the plasma membrane via endocytosis are also sent to lysosomes, where their contents — fluid and molecules from the extracellular environment — are processed. The process of endocytosis is an example of reverse vesicle trafficking, and it plays an important role in nutrition and immunity as well as membrane recycling. Lysosomes break down and thus disarm many kinds of foreign and potentially pathogenic materials that get into the cell through such extracellular sampling. 57 Unit 5: Plant Cells Have Chloroplasts and Other Structures Not Present in Animal Cells Plant cells have several structures not found in other eukaryotes. In particular, organelles called chloroplasts allow plants to capture the energy of the Sun in energy-rich molecules; cell walls allow plants to have rigid structures as varied as wood trunks and supple leaves; and vacuoles allow plant cells to change size. What Is the Function of Chloroplast Membranes? Chloroplasts are surrounded by two membranes. The outer membrane is permeable to small organic molecules, whereas the inner membrane is less permeable and studded with transport proteins. The innermost matrix of chloroplasts, called the stroma, contains metabolic enzymes and multiple copies of the chloroplast genome. Chloroplasts also have a third internal membrane called the thylakoid membrane, which is extensively folded and appears as stacks of flattened disks in electron micrographs. The thylakoids contain the light-harvesting complex, including pigments such as chlorophyll, as well as the electron transport chains used in photosynthesis. What Are Vacuoles? Plant cells additionally possess large, fluid-filled vesicles called vacuoles within their cytoplasm. Vacuoles typically compose about 30 percent of a cell's volume, but they can fill as much as 90 percent of the intracellular space. Function: 1. Plant cells use vacuoles to adjust their size and turgor pressure. Vacuoles usually account for changes in cell size when the cytoplasmic volume stays constant. 2. Some vacuoles have specialized functions, and plant cells can have more than one type of vacuole. Vacuoles are related to lysosomes and share some functions with these structures; for instance, both contain degradative enzymes for breaking down macromolecules. 3. Vacuoles can also serve as storage compartments for nutrients and metabolites. For instance, proteins are stored in the vacuoles of seeds. 4. rubber and opium are metabolites that are stored in plant vacuoles. 58 What Is the Cell Wall? Besides the presence of chloroplasts, another major difference between plant and animal cells is the presence of a cell wall. The cell wall surrounds the plasma membrane of plant cells and provides tensile strength and protection against mechanical and osmotic stress. It also allows cells to develop turgor pressure, which is the pressure of the cell contents against the cell wall. Plant cells have high concentrations of molecules dissolved in their cytoplasm, which causes water to come into the cell under normal conditions and makes the cell's central vacuole swell and press against the cell wall. With a healthy supply of water, turgor pressure keeps a plant from wilting. In drought, a plant may wilt, but its cell walls help maintain the structural integrity of its stems, leaves, and other structures, despite a shrinking, less turgid vacuole. The structure of cell wall The presence of the cell wall in plant cells distinguishes plants from animal cells. It determines the shape of the cell and the texture of the tissue. Cell walls have supportive and protective functions. Plant tissues in which the cell wall is thin and soft, as those of fruits, leaves, and fleshy stems and roots are commonly eaten by man and animals. Tissues in which the walls are thickened and strong or hard may be used as textiles, lumber, or other durable plant products. 59 The Cell Wall Layers: 1- The middle lamella It is found between the primary cell walls of neighboring cells. It is composed mainly of pectic compound combined with calcium. 2- The primary cell wall It is the first true cell wall which develops on the new cell. The primary cell wall is initially relatively plastic. It becomes gradually more rigid as the cell ages and enlarges. The primary cell wall contains cellulose, hemicellolose and some pectin. It may become lignified. 3- The secondary cell wall It is laid down between the primary cell wall and the plasma membrane and may become much thicker than the primary cell wall. It consists mainly of cellulose and hemicelluloses. Deposition of lignin and other substances occur in many cells. Generally, secondary walls are laid down after the primary wall ceases to increase in surface area. The secondary cell wall adds strength and rigidity to the cell. Pits Certain portions of the cell wall remain thin even as the secondary wall is formed, and they consist only of primary wall material. The primary pit fields of living cells are characterized by the presence of thin protoplasmic strands i.e., plasmodesmata. A pit consists of a pit cavity and a pit membrane. The pit cavity is open internally to the lumen of the cell and is closed by the pit membrane along the line of contact of two cells. 60 There are two main types of pits: 1- Simple pits In the simple pit, the secondary wall does not form an arch. Simple pits may be found in certain parenchyma cells, in fibers and in sclerides. 2- Bordered pits The main characteristic of bordered pits is that the secondary wall develops over the pit cavity to form an arch. Bordered pits occur mainly in the water-conducting and mechanical cells of the xylem such as vessel elements and tracheids. Plasmodesmata These are cytoplasmic strands interconnecting the living protoplasts of the plant body into an organic mass. They are thought to be concerned with material transport and conduction of stimuli. 61