Campbell Note PDF - Themes in the Study of Life

Chapter 1: Themes in the Study of Life Biology: The scientific study of life. Evolution: the process of change that has transformed life on Earth from its earliest beginnings to the diversity Systems Biology: Construct models of organisms living today....

Chapter 1: Themes in the Study of Life Biology: The scientific study of life. Evolution: the process of change that has transformed life on Earth from its earliest beginnings to the diversity Systems Biology: Construct models of organisms living today. for the dynamic behavior of who Properties of life: Order, Evolutionary Adaption, Response to the Environment, Regulation, Energy biological systems. processing, Growth and Development, Reproduction. 1. Themes connect the concepts of Biology Reductionism: the reduction of 1. New properties emerge at each level in the biological hierarchy (emergent properties). Thus, the study of complex systems to simpler life can be divided into different levels of biological organisation. components that are more 2. Organisms interact with their environments, exchanging matter and energy: cycling of nutrients, flow of manageable to study. energy. Work requires a source of energy 3. Structure and function are correlated at all levels of biological organization. 4. Cells are an organism’s basic units of structure and function. 5. The continuity of life is based on heritable information in the form of DNA 1. Genes: the units of inheritance that transmit information from parents to offspring. 2. DNA: the substance genes are made of. 3. Genome: The entire “library” of genetic instructions that an organism inherits. 6. Feedback mechanism regulate biological systems. 1. Negative feedback: Accumulation of an end product of a process slows that process. Eukaryotic cell is subdivided by 2. Positive feedback: Accumulation of an end product of a process speeds up that process. internal membranes. 2. The Core Theme: Evolution accounts for the unity and diversity of life Prokaryotic cell: DNA is not 1. Organizing the diversity of life separated from the rest of the cell in a nucleus. 1. The Three Domains of Life: Domain Bacteria and domain Archaea are prokaryotic. Domain Eukarya is eukaryotic. 2. Domain Eukarya is further divided into the kingdoms Protista, Plantea, Fungi, and Animalia. 2. Charles Darwin and the Theory of Natural Selection. 1. Nov. 1859: Charles Robert Darwin publishes On the Origin of Species by Means of Natural Selection. Inquiry: a search for information and 2. “Decent with modification” and “natural selection” explanation 3. The Tree of Life Data: Recorded observations Hypothesis: a tentative answer to a 1. Biologists’ diagrams of evolutionary relationships generally take treelike forms. well-framed question. 3. Scientists use two main forms of inquiry in their study of nature Theory: Much broader in scope than 1. Discovery science (descriptive science): Describing natural structures and processes as accurately as a hypothesis, is general enough to possible through careful observation and analysis of data. spin off many new, specific 1. Inductive reasoning: Deriving generations from a large number of specific examples. hypotheses, generally supported by a 2. Hypothesis-based science: Explaining nature. much greater body of evidence. 1. Deductive reasoning: From general premises, we extrapolate to the specific results we should Technology:applied scientific expect if the premises are true. knowledge for some specific purpose 2. Hypotheses must be testable and falsifiable. 3. Scientific method: The way scientists conduct experiments. 1. Controlled experiment: Compares an experimental group with an control group. 4. Scientific Models: A tool used to help explain a scientific concept. Chapter II: The Chemical Context of Life Living organisms are subject to basic laws of physics and chemistry. atom: the smallest unit of matter that still retains the properties of an element. 1. Matter consists of chemical elements in pure form and in combinations called compounds 1. Matter: anything that takes up space and has mass. Dalton: a unit of measurement the 2. Element: a substance that cannot be broken down to other substances by chemical reactions. same as the amu. 3. Compound: a substance consisting of two or more different elements combined in a fixed ratio. Energy: the capacity to cause 4. About 25% of the 92 elements are essential to life. change. 5. Carbon, Hydrogen, Oxygen and Nitrogen make up 96% of living matter. 6. Most of the remaining 4% is made up of phosphorous, potassium, and sulfer. Potential energy: the energy that 7. Trace elements: elements required by an organism in only minute quantities. matter possesses because of its 2. An element’s properties depend on the structure of its atoms location or structure. 1. Subatomic particles: neutrons (N), protons (+), electrons (-). Protons and neutrons are tightly packed together in the atomic nucleus. 2. Atomic number: the number of protons in the nuclei of an atom. 3. Mass number: the sum of the protons plus neutrons in the nucleus of an atom. 4. Atomic mass: the mass of an atom (in daltons) 5. Isotope: the different atomic forms of an element. A radioactive isotope is one in which the nucleus Chemical bonds: Interactions that decays spontaneously. hold atoms together. 6. Electron shells: where electrons are found. Valence: the number of unpaired 1. Valence electrons are the outermost electrons and they are found in the valence shell. electrons required to complete an 2. Orbital: the three-dimensional space where an electron is found 90% of the time. The first shell atom’s outermost shell. only has 1 s orbital. The second shell has 1 s orbital and 3 p orbitals. The third shell has more complex orbitals. Electronegativity: The attraction of a particular kind of atom for the 3. The formation and function of molecules depend on chemical bonding between atoms electrons of a covalent bond. 1. Covalent bond: the sharing of a pair of valence electrons by two atoms. 1. Molecule: two or more atoms held together by covalent bonds. Shulin Ye pg 1 of 2 08/31/09 07:28:04 PM  Chapter 2: The Chemical Context of Life Ion: a charged atom or molecule 2. Single bond: only one pair of electrons shared. Cation: Positively charged ion 3. Structural Formula: A way of representing molecular structure. Ex... H—H Anion: Negatively charged ion 4. Molecular Formula: Indicates what atoms are in a molecule. Ex.... H2 5. Double bond: two pairs of electrons shared. 6. Nonpolar covalent bond: Electrons are shared equally 7. Polar covalent bond: Electrons are shared equally. 2. Ionic Bonds: In some cases, two atoms are so unequal in their attraction for valence electrons that the more electronegative atom strips an electron completely away from its partner. An ionic bond is formed when cations and anions attract each other. 1. Compounds formed by ionic bonds are called ionic compounds or salts. 2. The formula for an ionic compound indications only the ratio of elements in a crystal of the salt. 3. Weak Chemical Bonds 1. Hydrogen Bond: Formed when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom. In living cells, the electronegtaive atom is usually nitrogen or oxygen. 2. van der Waals interactions: When atoms, by chance, become slightly polarized and molecules stick together slightly. Very weak force, but allows geckos to walk up a wall. 4. Molecular Shape and Function Chemical reactions: the making and 1. A molecule has a characteristic size and shape, determined by the positions of the atoms’ orbitals. breaking of chemical bonds. The shape of the molecule is very important to its function. Molecules with similar shapes have Reactants: starting materials similar biological effects. Products: ending materials. 2. For water (H20), the molecule is shaped like a V with its two covalent bonds spread apart at an Chemical equilibrium: the point at angle of 104.5º which the reactions offset one 3. The methane molecule (CH4) has the shape of a completed tetrahedron because all four hybrid another equally orbitals of carbon are shared with hydrogen atoms. 4. Only molecules with complementary shapes can form weak bonds with each other. 4. Chemical Reactions Make and Break Chemical Bonds 1. All atoms of the reactants must be accounted for in the products: Reactions cannot create or destroy matter but can only rearrange it. 2. All chemical reactions are reversible, with the products of the forward reaction becoming the reactants for the reverse reaction. Shulin Ye pg 2 of 2 08/31/09 07:28:04 PM  Chapter 3: Water and the Fitness of the Environment Cells are about 70-95% water 2. The Polarity of Water Molecules Results in Hydrogen Bonding Polar Molecule: A molecule in 1. Water is a polar molecule. The slightly positive hydrogen of one molecule is attracted to the slightly which the two ends of the molecule negative oxygen of a nearby molecule. have opposite charges. 3. Four emergent properties of water contribute to Earth’s fitness for life Adhesion: The clinging of one 1. Cohesion: a phenomenon that appears because hydrogen bonds hold water together. substance to another 1. Cohesion due to hydrogen bonding contributes to the transport of water and dissolved nutrients Surface tension: a measure of how against gravity in plants. difficult it is to stretch or break the 2. Water also has a greater surface tension than most other liquids. surface of a liquid. 2. Moderation of Temperature: Water moderates air temperature by absorbing heat from air that is warming Kinetic energy: the energy of and releasing the stored heat to air that is cooler. Water is good for heat storage because it has a high motion. specific heat. Heat: a measure of the matter’s total 1. Calorie: the amount of heat it takes to raise the temperature of 1 g of water by 1ºC. kinetic energy due to motion of its molecules. Depends on the volume. 2. Joule: The work exerted when one applies a force of one newton to move an object 1m. 1 calorie Temperature: a measure of heat equals 4.184 joules. intensity that represents the average 3. Specific Heat: the amount of heat that must be absorbed or lost for 1g of a substance to change its kinetic energy of the molecules, temperature by 1ºC. regardless of volume. 1. Water’s high specific heat is due to the hydrogen bonding that requires a lot more energy to break. This can moderate temperature near and in large bodies of water. Heat of vaporization: the quantity of 4. Evaporative Cooling: as a liquid evaporates, the surface of the liquid that remains behind cools heat a liquid must absorb for 1 g of it down. to be converted from the liquid to the 1. Water’s high heat of vaporization is another emergent property caused by hydrogen bonds, gaseous state. which must be broken before the molecules can make their exodus from the liquid. 2. Evaporative cooling of water contributes to the stability of temperature in lakes and ponds and also provides a mechanism that prevents terrestrial organisms from overheating. 3. Insulation of Bodies of Water by Floating Ice 1. Water is one of the few substances that are less dense as a solid than as a liquid. This is because hydrogen bonding locks solid water into a crystalline lattice and holds the molecules slightly apart. Water actually reaches its greatest density at 4ºC. Ice at 0ºC is actually 10% less dense than liquid water at 4ºC. 2. Because ice floats on top of water, it insulates the water below it and prevents deep bodies of water from freezing completely, allowing life to survive under the frozen surface. Solution: a liquid that is a completely 4. The Solvent of Life. homogeneous mixture of two ore 1. Water is the best solvent out there, but it is not a universal solvent. more substances. 2. Hydration shell: the sphere of water molecules around each dissolved ion. Aqueous solution: one in which 3. Hydrophilic: Any substance that has an affinity for water. Substances can be hydrophilic without water is the solvent. actually dissolving if the molecules are large enough. Solvent: the dissolving agent. 4. Colloid: a stable suspension of fine particles in a liquid. Solute: the substance that is 5. Hydrophobic: Substances that seem to repel water. dissolved. 6. Molecular Mass: the sum of the masses of all the atoms in a molecule. 7. Mole (mol): represents an exact number of objects—6.022 x 1023. 8. Molarity: the number of moles of solute per liter of solution. 4. Acidic and basic conditions affect living organisms 1. Occasionally, a hydrogen atom participating in a hydrogen bond between two water molecules shifts from one molecule to the other. The hydrogen leaves its electron behind. 1. Hydroxide ion: OH- ; Hydronium ion:H3O+. By convention, it’s represented by H+, even though H+ Acid: a substance that increases the does not exist on its own in an aqueous solution. OH- and H+ are very reactive. hydrogen ion concentration of a 2. This is a reversible reaction. In pure water, only one water molecule in every 554 million is solution. dissociated. Base: a substance that reduces the 3. Biologists use the pH scale to describe how acidic or basic a solution is. hydrogen ion concentration of a 2. Strong acids and bases completely dissociate in water. Ex. HCl and NaOH. Weak acids and bases solution. reversibly release and accept back hydrogen ions. Ex. NH4 and H2CO3. pH: the negative common logarithm 3. In any aqueous solution at 25ºC, the product of the H+ and OH- concentrations is constant at 10-14. of the hydrogen ion concentration: 4. The internal pH of most living cells is close to 7. The pH of human blood is very close to 7.4. A person pH=-log[H+]. The lower the number, cannot survive for more than a few minutes if the blood pH drops to 7 or rises to 7.8. Buffers are the more acid the solution. Most substances that minimize changes in the concentrations of H+ and OH- in a solution. biological fluids are within the range 5. Considering the dependence of all life on water, contamination of rivers, lakes, seas and rain is a dire pH 6-8. environmental problem. Acid precipitation refers to rain, 6. Carbon dioxide, the main product of fossil fuel combustion, also causes other problems. It is one of the snow or fog with a pH lower than pH 5.2. It affects lakes, streams and soil chemicals implicated in global warming. adversely. 7. When CO2 dissolves in seawater, it reacts with water (H2O) to form carbonic acid (H2CO3). Almost all of the carbonic acid in turn dissociates, producing protons and a balance between two ions, bicarbonate (HCO3-) and carbonate (CO32-). As seawater acidifies due to the extra protons, the balance shifts towards HCO3-, lowering the concentration of CO32-. Because calcification is directly affected by the concentration of CO32-, any decrease in CO32- is therefore of great concern because calcification accounts for the formation of coral reefs in our tropical seas. The expected doubling of CO2 emissions by the year 2065 could lead to a 40% decrease in coral reef calcification, according to a study by Chris Langdon and colleagues. Shulin Ye pg 1 of 2 08/31/09 07:28:04 PM  Chapter 4: Carbon and the Molecular Diversity of Life Organic chemistry: the study of 1. Organic chemistry is the study of carbon compounds compounds containing carbon. Of all 1. The science of organic chemistry originated in attempts to purify and improve the yield of other chemical elements, carbon is organisms. unparalleled in its ability to form 2. Early 1800s: chemists could make many simple compounds but could not synthesize the complex molecules that are large, complex, molecules extracted from living matter. and diverse. 3. 1828: Friedrich Wöhler attempted to make ammonium cyanate by mixing solutions of ammonium ions ( Vitalism: the belief in a life force ¿ outside the jurisdiction of physical NH 4 ) and cyanate ions (CNO-). However, he managed to make urea instead. and chemical laws 4. Hermann Kolbe, a student of Wöhler’s made the organic compound acetic acid from inorganic Mechanism: the view that physical substances that could be prepared directly from pure elements. and chemical laws govern all natural 5. 1953: Stanley Miller helped bring this abiotic synthesis of organic compounds into the context of phenomena. evolution by simulating the early earth. 6. All this discredited vitalism and supported mechanism. 2. Carbon atoms can form diverse molecules by bonding to four other atoms 1. The key to an atom’s chemical characteristics is its electron configuration. This configuration determines the kinds and number of bonds an atom will form with other atoms. 2. Carbon usually completes its valence shell by sharing its 4 valence electrons. When a carbon atom forms four single covalent bonds, the bonds angle towards the corners of an imaginary tetrahedron. When two carbon atoms are joined by a double bound, however, all bonds around those carbons are in the same plane. Hydrocarbons: organic molecules 3. Carbon chains form the skeletons of most organic molecules. The skeletons vary in length and may be consisting of only carbon and straight, branched or arranged in closed rings. hydrogen. They can release a 4. Isomers: compounds that have the same numbers of atoms of the same elements but different structures relatively large amount of energy. and hence different properties. 1. Structural isomers differ in the covalent arrangements of their atoms. 2. Geometric isomers have the same covalent partnerships, but they differ in their spatial arrangements. 3. Enantiomers are isomers that are mirror images or each other. 3. A small number of chemical groups are key to the functioning of biological molecules 1. The distinctive properties of an organic molecule molecule also depend on the molecular components attached to the carbon skeleton. 2. Functional Group: the chemical groups affect molecular function by being directly involved in chemicals reactions. Shulin Ye pg 2 of 2 08/31/09 07:28:04 PM  Chapter 5: The Structure and Function of Large Biological Molecules. Macromolecules: enormous 1. Macromolecules are polymers, built from monomers: molecules that can have a mass well 1. Polymer: long molecule consisting of many similar or identical building blocks (monomers) linked by covalent bonds. over 100,000 amu. Monomers are joined by dehydration reactions, which are facilitated by enzymes. The reverse reaction of dehydration synthesis is hydrolysis. 2. Carbohydrates serve as fuel and building material 1. Carbohydrates include both sugars and polymers of sugars. 2. The simplest carbohydrates are monosaccharides, which usually have empirical formulas of CH2O. Glucose is the most common monosaccharide. It has a carbonyl group and multiple hydroxyl groups. Monosaccharides are classified by the number of carbon atoms and the location of the carbonyl groups. 1. In aqueous solutions, most sugar molecules will form rings. 2. Monosaccharides are major nutrients. Not only are they a major fuel for cellular work, they also serve as the raw material for the synthesis of other organic molecules. 3. A disaccharide consists of two monosaccharides joined by a glycosidic linkage. 4. Polysaccharides are macromolecules formed monosaccharides. They are generally used as energy storage and as structural materials. 1. Plants tend to store starch, a polymer of glucose monomers. Starch is made of alpha-glucose and is helical. Generally, starch has few to no branching. The unbranched version is amylose; the branched version is amylopectin. 2. Animals store glycogen, a more highly branched glucose polymer, instead. 3. Cellulose is a major component of the tough walls that enclose plant cells. Because it is made of beta-glucose, the molecule is straight, and hydrogen-bonding between parallel cellulose molecules hold them together. About 80 cellulose molecules associate to form a microfibril, which weaves itself into the cell wall. Very few things can digest cellulose. 4. Chitin: the carbohydrate used by arthropods to build their exoskeletons and fungi to build their cell ways. 3. Lipids are a diverse group of hydrophobic molecules 1. Fats are constructed from glycerol, an alcohol with three carbons, each bearing a hydroxyl group; and fatty acids, long chains of carbon with a carboxyl group at one end. Fats separate water because the water molecules hydrogen-bond to each other and exclude the fats. Three fatty acids each join to a glycerol with ester linkages, forming a triacylglycerol. 1. Saturated fatty acid-contains only single bonds between the carbon molecules. Usually solid at room temperature. 2. Unsaturated fatty acid-contains one or more double bonds. A cis double bond creates a kink in the molecule, preventing the molecules from packing too tightly together so they are liquid at room temperature. 3. Major function of fats is energy energy storage, insulation, and cushioning. 2. Phospholipids make up the cell membranes. They have two fatty acids joined to a glycerol; the third hydroxyl group of glycerol is joined to a phosphate group. The fatty acids are hydrophobic, the phosphate group is hydrophilic. In water, phospholipids form a lipid bilayer to keep the fatty acid tails away from water. 3. Steroids: lipds characterized by a carbon skeleton consisting of four fused rings. 1. Cholesterol is a common component of animal cell membranes and is also the precursor from which other steroids are synthesized. 4. Proteins have many structures, resulting in a wide range of functions 1. Proteins account for more than 50% of the dry mass of most cells. Some proteins speed up chemical reactions, while Enzymes: biological catalysts. Most others play a role in structural support, storage, transport, cellular communication, movement, and defense against are proteins. foreign substances. Amino acids: organic molecules 2. All proteins are polymers constructed from the same set of 20 amino acids. A protein consists of one or polypeptides. A possessing both carboxyl and amino functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into groups. a molecule of unique shape. There are four levels of protein structure: 1. Primary structure: the unique sequence of amino acids. 2. Secondary Structure: either a coil (alpha-helix) or folds (beta-pleated sheet) that result from the hydrogen bonds between the repeating constituents of the polypeptide backbone. 3. Tertiary structure: the overal shape of a poly peptide resulting from interactions between the side chains (R groups). 1. Hydrophobic interaction: water molecules exclude non-polar substances as they form hydrogen bonds with each other and the hydrophilic parts of the protein. Non-polar amino acids then attract each other with van der Waals intercations. 2. Polar side chains and ionic bonds: form between positively and negatively charged side chains to help X-ray crystallography: A method stabilize tertiary structure. used to figure out the structure of 3. Disulfide bridges: the sulfur of cysteine bonds to the sulfur of another cysteine. molecules. 4. Quaternary structure: the overall protein strcture that results from the aggregation of several polypeptide subunits. Nuclear Magnetic Resonance 3. Proteins are joined by dehydration synthesis, which forms peptide bonds. spectroscopy: A method used to 4. Denaturation: the processes that causes a protein to lose its structure and function. figure out the structure of molecules 5. Chaperonins: proteins molecules that assist in the proper folding of other proteins. which does not require crystallization. Bioinformatics: Predicting the 3D structure of proteins from their amino acid sequences. Shulin Ye pg 1 of 2 08/31/09 07:28:04 PM  Chapter 5: The Structure and Function of Large Biological Molecules. Gene: a unit of inheritance. Codes 5. Nucleic acids store and transmit hereditary information for the amino acid sequence of a 1. Nucleic acids: enable living organisms to reproduce their complex components from one generation to the next. There polypeptide. are two types: 1. Deoxyribonucleic acid 2. Ribonucleic acid 2. Sites of protein synthesis are tiny structures called ribosomes. 3. Nucleic acids are macromolecules that exist as polymers called polynucleotides, which consist of monomers called nucleotides. 1. There are two types of nucleotides: 1. pyrimidines, which have a six-membered ring of carbon and nitrogen atoms. They include cytosine, thymine, and uracil. 2. Purines: which have a six-membered ring fused to a five-membered ring. They include adenine and guanine. 2. The sugars connected to the nitrogenous base are ribose and deoxyribose; the later lacks an oxygen atom on the second carbon of its ring. Because the atoms in both the nitrogenous base and the sugar are numbered, the sugar atoms have a prime (') after the number to distinguish them. 3. Adjacent nucleotides are joined by a phosphodiester linkage. The two free ends of the polymer are distinctly different from each other. One end has a phosphate attached to a 5’ carbon, and the other end has a hydroxyl group on the 3’ carbon. 4. DNA molecules have two polynucleotides that spiral around an imaginary axis, forming a double helix. 1. The two sugar-phosphate backbones run in opposite 5’→3’ directions from each other, an arrangement referred to as antiparallel. 2. One long DNA double helix includes many genes. 3. Adenine always pairs with thymine, and guanine always pairs with cytosine (in DNA). 5. The linear sequences of nucleotides in DNA molecules are passed from parents to offspring. Siblings have greater similarity in their DNA and proteins than do unrelated individuals of the same species. 6. Molecular biology has added a new tape measure to the toolkit biologists use to assess evolutionary kinships. Shulin Ye pg 2 of 2 08/31/09 07:28:04 PM  Chapter 6: A Tour of the Cell Light microscope: visible light is 1. To study cells, biologist use microscopes and the tools of biochemistry passed through the specimen and 1. 1665: Robert Hooke sees cell walls from the bark of an oak tree. then through glass lenses. Cannot 2. 1674: Antoni van Leeuwenkoek sees living cells. resolve detail finer than about 200 3. Organelles: Membrane-enclosed compartments within cells. nanometers. 4. Scanning electron microscope: The electron beam scans the surface of the sample, which is usually coated with gold. Electron Microscope: Focuses a The beam excites electrons on the surface, and these secondary electrons are detected by a device that translates the beam of electrons through the pattern of electrons into an electronic signal to a video screen. specimen or onto its surface. For 5. Transmission electron microscope: aims an electron beam through a very thin section of the specimen, similar to the practical purposes they usually way a light microscope transmits light through a slide. The specimen has been stained with atoms of heavy metals, cannot resolve biological structure which attach to certain cellular structures, thus enhancing the electron density of some parts of the cell more than others. smaller than about 2 nm. Invented in The electrons passing through the specimen are scattered more in the denser regions, so fewer are transmitted. the 1950s. Disadvantage: the 6. Microscopy techniques can introduce artifacts, structural features seen in micrographs that do not exist in the living processes to prepare the slides kills cells. them. Cell fractionation: takes cells apart and separates the major organelles and other subcellular structures from one another. 2. Eukaryotic cells have internal membranes that compartmentalize their functions cytosol: the aqueous part of the 1. All cells have several basic features in common: cytoplasm within which various 1. They are all bounded by selective membrane called the plasma membrane. particles and organelles are 2. They contain chromosomes, which carry genes in the form of DNA. suspended 3. They have ribosomes, which make proteins according to instructions from the genes. 2. In eukaryotic cells: 1. Most of the DNA is in an organelle called the nucleus, which is bounded by a double, porous membrane. 2. Have membrane-bound organelles. These provide different local environments that facilitate specific metabolic functions. 3. In prokaryotic cells: 1. the DNA is concentrated in a region that is not membrane-enclosed, called the nucleoid. 2. Lack membrane-bound organelles. 4. The plasma membrane functions as a selective barrier that allows sufficient passage of oxygen, nutrients and wastes to service the entire cell. Like most biological membranes, plasma membranes consist of a double layer of phospholipids and other lipids. 3. The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes 1. The nuclear envelope, which encloses the nucleus, is a double membrane. Each membrane is a lipid bilayer and the two are separated by a space of about 20-40 nm. The envelope has many pores. At the lip of each pore, the inner and Nucleus: contains most of the genes outer membranes are continuous. A pore complex, made out of proteins, lines each pore and regulates the entry and exist in the eukaryotic cell. of proteins, RNAs, and macromolecules. Nuclear lamina: a netlike array of 2. Chromosomes: structures that carry genetic information. Each chromosome is made of chromatin. protein filaments that maintains the 3. Nucleous: a mass of densely stained granules fibers in the nucleus that synthesizes rRNA. same of the nucleus by mechanically 4. The nucleus directs protein synthesis by synthesizing mRNA according to instructions provided by the DNA. The supporting the nuclear envelope. mRNA is then transported to the cytoplasm via the nuclear pores. Once an mRNA molecule reaches the cytoplasm, ribosomes translate the mRNA’s genetic message into the primary structure of a specific polypeptide. Nuclear matrix: a framework of fibers extending throughout the 5. Free ribsomes are suspended in the cytosol while bound ribosomes are attached to the outside of the endoplasmic nuclear interior. reticulum or nuclear envelope. Most of the proteins made by free ribosomes function within the cytosol. Bound ribosomes generally make proteins that are destined for insertion into membranes, for packaging within certain organelles such as lysosomes, or for export from the cell. Endomembrane system: synthesizes 4. The endomembrane system regulates protein traffic and performs metabolic functions in the cell. proteins, transports proteins into 1. The membranes of the endomembrane system are related either through direct physical continuity or by the transfer of membranes and organelles or out of membrane segments as tiny vesicles. the cell, metabolism and movement 2. The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, lysosomes, of lipids, and detoxification of various kinds of vacuoles, and the plasma membrane. poisons. 3. Endoplasmic reticulum: accounts for more than half the total membrane in many eukaryotic cells. The ER consists of a network of membranous tubules and sacs called cisternae. The ER membrane separates the internal compartment of the ER, called the ER lumen or cisternal space, from the cytosol. The ER membrane is continuous with the nuclear envelope. The space between the two membranes of the nuclear envelope is continuous with the lumen of the ER. 4. The smooth ER synthesizes lipids, including oils, phospholipids, and steroids. Other enzymes of the smooth ER help Transport vesicles: vesicles in detoxify drugs and poisons, especially in liver cells. The smooth ER also stores calcium ions. transit from one part of the cell to 5. Many types of cells secrete proteins produced by ribosomes attached to rough ER. As a polypeptide chain grows from a another. bound ribosomes, it is threaded into the ER lumen through a pore formed by a protein complex in the ER membrane. Most secretory proteins are glycoproteins. Secretory proteins depart from the ER wrapped in the membranes of vesicles that bud like bubbles from a specialized region called the transitional ER. 6. Rough ER is also a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane. 7. After leaving the ER, many transport vesicles travel to the Golgi apparatus, where products of the ER are modified, stored, and sent to other destinations. The Golgi apparatus consists of flattened membranous sacs—cisternae--looking like a stack of pita bread. Vesicles concentrated in the vicinity of the of the Golgi apparatus are engaged in the transfer of material between parts of the Golgi and other structures. The two poles of a Golgi stack are referred to as the cis face, which receives material, and the trans face, which ships material. The cis face is usually located near the ER. The trans face gives rise to vesicles, which pinch off and travel to other sites. Products of the ER are usually modified during their transit from the cis region to the trans region of the Golgi. The Golgi apparatus also manufactures certain macromolecules by itself, such as pectins and other noncellulose polysaccharides. The Golgi manufactures and refines its products in stages, with different cisternae containing unique teams of enzymes. Before a Golgi stack dispatches its products by budding vesicles from the trans face, it sorts these products and targets them for various parts of the cell. 8. Lysosomes: a membranous sac of hydrolytic enzymes that an animal cell uses to digest macromolecules. Hydrolytic enzymes and lysosomal membrane are made by rough ER and then transferred to the Golgi apparatus for further processing. 1. Amoebas and many other protists eat by engulfing smaller organisms or other food particles, a process called phagocytosis. The food vacuole formed in this way then fuses with a lysosome, whose enzymes digest the food. Shulin Ye pg 1 of 3 08/31/09 07:28:04 PM  Chapter 6: A Tour of the Cell 2. Autophagy: the process in which lysosomes use their hydrolytic enzymes to recycle the cell’s own organic material. 3. In plants and fungi, which lack lysosomes, vacuoles carry out hydrolysis. 4. In Tay-Sachs disease, a lipid-digesting enzyme is missing or inactive, the lysosomes become engorged with lipids and begin to interfere with other cellular activities. This causes the brain to become impaired by an accumulation of lipids in the cells. Food vacuoles: store food 9. Vacuoles: Diverse Maintenance Compartments. Contractile vacuoles: pump water 1. Mature plant cells generally contain a large central vacuole. The solution inside, called cell sap, differs in out of cell. composition from the cytosol. The central vacuole can hold reserves of important organic compounds, inorganic ions, and can also contain metabolic by-products, pigments, or poisons to prevent predators. Vacuoles also help plants grow faster by absorbing water. 5. Mitochondria and chloroplasts change energy from one form to another 1. Mitochondria have two membranes separating their innermost space from the cytosol, and chloroplasts typically have Mitochondria: sites of cellular tree. (Chloroplasts and related organelles in some algae have four membranes.) The membrane proteins of mitochondria respiration. and chloroplasts are made not by ribosomes bound to the ER, but by free ribosomes in the cytosol and by ribosomes contained within these organelles themselves. Mitochondria and chloroplasts also contain a small amount of DNA. They are semi-autonomous organelles that grow and reproduce within the cell. 2. Mitochondria are found in nearly all eukaryotic cells. They are about 1-10 µm long. Time-lapse films of living cells reveal mitochondria moving around, changing their shapes, and fusing or diving into two. The mitochondrion is enclosed by two membranes, each phospholipid bilayer with a unique collection of embedded proteins. The outer membrane is smooth, but the inner membrane is convoluted, with infoldings called cristae. 1. Intermembrane space: the narrow region between the inner and outer membranes. 2. Mitochondrial matrix: is enclosed by the inner membrane and contains mitochondrial DNA and ribosomes, in addition to many different enzymes. Chloroplasts: sites of photosynthesis 3. The chloroplast is a specialized member of a family of closely related plant organelles called plastids. Chloroplasts contain the green pigment chlorophyll, along with enzymes and other molecules that function in the photosynthetic production of sugar. Their shapes are changeable, and they grow and occasionally pinch in two, reproducing themselves. 1. Thylakoids: flattened, interconnected sacs inside chloroplasts. They are sometimes arranged into stacks called grana. The fluid outside the thylakoids is the stroma, which contains the chloroplast DNA and ribsomes as well as many enzymes. The membranes of the chloroplast divide the chloroplast space into three compartments: the intermembrane space, the stroma, and the thylakoid space. 4. The peroxisome is a specialized metabolic compartment that is bounded by a single membrane. They contain enzymes that transfer hydrogen from various substrates to oxygen, producing hydrogen peroxide as a by-product, from which the organelle derives its name. Some peroxisomes use oxygen to break fatty acids down. Peroxisomes in the liver detoxify alcohol and other harmful compounds. H2O2 itself is toxic, but peroxisomes also contains an enzyme that converts it to Peroxisome: oxidative organelle that water. is not part of the endomembrane 1. Specialized peroxisomes called glyoxysomes are found in the fat-storing tissues of plant seeds. They convert fatty system. Imports its proteins primarily acids to sugar. from the cytosol. 2. Peroxisomes do not bud from the endomembrane system. They grow larger by incorporating proteins made primarily in the cytosol, lipids made in the ER, and lipids synthesized within the peroxisome itself. They may increase in number by splitting in two when they reach a certain size. Cytoskeleton: a network of fibers 6. The cytoskeleton is a network of fibers that organizes structures and activities in the cell extending throughout the cytoplasm. 1. The cytoskeleton plays a major role in organizing the structures and activities of the cell, is composed of three types of molecular structures: microtubules, microfilaments, and intermediate filaments. 1. Microtubules are the thickest of the three types. They are hollow rods measuring about 25 nm in diameter and from 200 nm to 25 µm in length. They are constructed of tubulin proteins. Each tubulin protein is a dimer, a molecule made up of two subunits. One end of the microtubule can accumulate or release tubulin dimers at a much higher rate than the other, thus growing and shrinking significantly during cellular activities. This is called the “plus end”. Microtubules shape and support the cell and also serve as tracks along which organelles equipped with motor proteins can move. They resist compression forces. 1. In animal cells, microtubules grow out from a centrosome, a region that is often located near the nucleus and is considered a “microtubule-organizing center.” Within the centrosome are a pair of centrioles, each composed of nine sets of triplet microtubules arranged in a ring. Although centrosomes with centrioles may help organize microtubule assembly in animal cells, they are not essential for this function in all eukaryotes. 2. A specialized arrangement of microtubules is responsible for the beating of flagella and cilia. Flagella and cilia can act as locomotor appendages or they can move fluid over the surface of a tissue. Motile cilia usually occur in large numbers of the cell surface. They are about 0.25 µm in diameter and about 2-20 µm long. Flagella are the same diameter but longer, 10-200 µm and are typically limited to just one or a few per cell. A flagellum has an undulating motion while cilia work more like oars. 1. A cilium may also act as a signal-receiving “antenna” for the cell. Cilia that have this function are generally nonmotile, and there is only one per cell. (In vertebrate animals, almost all cells seem to have such a cilium, which is called a primary cilium.). 2. Motile cilia and flagella share a common ultrastructure. Both have a core of microtubules sheathed in an extension of the plasma membrane. Nine doublets of microtubules, the members of each pair sharing part of their walls, are arranged in a ring. In the center of the ring are two single microtubules. Nonmotile primary cilia lack the central pair of microtubules. The microtubule assembly of a cilium or a flagellum is anchored in the cell by a basal body, which is structurally very similar to a centriole. 3. In flagella and motile cilia, flexible cross-linking proteins, even spaced along the length of the cilium or flagellum, connect the outer doublets to each other and to the two central microtubules. Each outer doublet also has pairs of protruding proteins, called dyneins, spaced along its length and reaching toward the neighboring doublet. The mechanics of dynein-based bending involve a process that resembles walking. A typical dynein protein has two “feet” that “walk” along the microtubule of the adjacent doublet, one foot maintaining contact while the other releases and reattaches one step further along the microtubule. Microtubule doublets seem to be to be held in place by cross-linking proteins just inside the outer doublets and by the radial spokes and other structural elements, so the forces exerted by dynein “walking” cause the doublets to curve. Shulin Ye pg 2 of 3 08/31/09 07:28:04 PM  Chapter 6: A Tour of the Cell 2. Microfilaments (also known as actin filaments) are the thinnest. They are solid rods about 7 nm in diameter and are made out of molecules of actin. A microfilament is a twisted double chain of actin subunits. Beside occurring as linear filaments, microfilaments can form structural networks. They seem to be present in all eukaryotic cells. They bear tension. A three-dimensional network formed by microfilaments (cortical microfilaments) just inside the plasma membrane helps support the cell’s shape. This network gives the out cytoplasmic layer of a cell (the cortex) the semisolid consistency of a gel. In animal cells specialized for transporting materials across the plasma membrane, bundles of microfilaments make up the core of microvilli. 1. Microfilaments are well known for their role in cell motility, particularly as part of the contractile apparatus of muscle cells. Contraction of the muscle cell results from the actin and myosin filaments sliding past one another. In other kinds of cells, actin filaments are associated with myosin in miniature and less elaborate versions of the arrangement in muscle cells. These actin-myosin aggregates are responsible for localized contraction of cell. A contracting belt of microfilaments forms a cleavage furrow that pinches a dividing animal cell into two daughter cells. Localized contraction also plays a role in amoeboid movement. In plant cells, both actin-myosin interactions and sol-gel transformations brought about by actin may be involved in cytoplasmic streaming. 3. Intermediate filaments have diameters in a middle range, 8 nm-12 nm. They are specialized for bearing tension. Each type is constructed from a different molecular subunit belonging to a family of proteins whose members include keratins. Intermediate filaments are more permanent fixtures of cells than are microfilaments and microtubules. Even after cells die, the intermediate filament networks often persist. Intermediate filaments are especially important in reinforcing the shape of a cell and fixing the position of certain organelles. The nucleus commonly sits within a cage of made of intermediate filaments. Other intermediate filaments make up the nuclear lamina. In cases where the shape of the entire cell correlated with function, intermediate filaments support that shape. 2. The most obvious function of the cytoskeleton is to give mechanical support to the cell and maintain its shape. The cytoskeleton provides anchorage for many organelles and even cytosolic enzyme molecules. It can be quickly dismantled in one part of the cell and reassembled in a new location, changing the shape of the cell. 3. Cell motility generally requires the interaction of the cytoskeleton with motor proteins. Vesicles and other organelles often travel to their destinations along “monorails” provided by the cytoskeleton. 4. The cytoskeleton is also involved in regulating biochemical activities in the cell in response to mechanical simulation. Cytoskeleton transmission of naturally occurring mechanical signals may help regulate and coordinate the cell’s response. 7. Extracellular components and connections between cells help coordinate cellular activities. Cell Wall: an extracellular structure 1. The plasma membrane is usually regarded as the boundary of the living cell, but most cells synthesize and secrete of plant cells that protects the cell, materials that are external to the plasma membrane. maintains its shape, and prevents 2. Plant cell walls are much ticker than the plasma membrane, ranging from 0.1 µm to several micrometers. The exact excessive uptake of water. chemical composition of the wall varies from species to species and cell type to cell type. Microfibrils made of the polysaccharide cellulose are secreted to the extra cellular space, where they become embedded in a matrix of other polysaccharides and proteins. 1. A young plant cell first secretes a relatively thin and flexible wall called the primary cell wall. In actively growing cell, the cellulose fibrils are oriented at right angles to the direction of cell expansion. Microtubules in the cell cortex guide cellulose synthase as it synthesized and deposits the fibrils. 2. Between the primary walls of adjacent cells is the middle lamella, a thin layer rich in sticky polysaccharides called pectin. It glues adjacent cells together. 3. When a plant cell matures and stops growing, it strengthens its wall. Some just secrete hardening substances into the primary cell wall. Others add a secondary cell wall between the plasma membrane and the primary wall. 3. Although animal cells lack walls akin to those of plant cells, they do have an elaborate extracellular matrix. The main ingredients of the ECM are glycoproteins secreted by the cells. The most abundant glycoprotein in the ECM of most animal cells is collagen, which forms strong fibers outside the cells. The collagen fibers are embedded in a network woven from proteoglycans. Some cells are attached to the ECM by still other ECM glycoproteins, such as fibronectin. Fibronectin and other ECM proteins bind to cell surface receptor proteins called integrins that are built into the plasm membrane. Integrins span the membrane and bind on their cytoplasmic side to associated proteins attached to microfilaments of the cytoskeleton. By communicating with a cell through integrins, the ECM can regulate a cell’s behavior. 4. Intercellular junctions 1. Plasmodesmata: The channels that perforate cell walls in plants. Cytosol passes through the plasmodesmata and connects the chemical environments of adjacent cells. The plasma membranes of adjacent cells line the channel of each plasmodesmata and thus are continuous. 2. In animals, there are three main types of intercellular junctions: tight junctions, desmosomes, and gap junctions. All three types of intercellular junctions are especially common in epithelial tissue. 1. Tight junctions: the plasma membranes of neighboring cells are very tightly pressed against each other, bound together by specific proteins. Tight junctions prevent leakage of extracellular fluid across a layer of epithelial cells. 2. Desmosomes function like rivets, fastening cells together into strong sheets. Intermediate filaments made of sturdy keratin proteins anchor desmosomes in the cytoplasm. Desmosomes attach muscle cells to each other. 3. Gap junctions provide cytoplasmic channels from one cell to an adjacent cell are are similar to plasmodesmata in plant cells. They consist of membrane proteins that surround a pore through which ions, sugars, amino acids, and other small molecules may pass. Shulin Ye pg 3 of 3 08/31/09 07:28:04 PM  Chapter 7: Membrane Structure and Function. Selective permeability: Some 1. Cellular membranes are fluid mosaics of lipids and proteins substances can cross easier than 1. The plasma membrane is the edge of life, the boundary that separates the living cell from its surroundings. others. 2. The most abundant lipids in most membranes are phospholipids, which are amphipathic molecules. 3. In the fluid mosaic model, the membrane is a fluid structure with a “mosaic” of various proteins embedded in or attached to a double layer (bilayer) of phospholipids. 4. 1915: membranes isolated from red blood cells were chemically analyzed and found to be composed of lipids and proteins. 5. 1925: Two Dutch scientists, E. Gorter and F. Grendel, reasoned that cell membranes must be phospholipid bilayers. 6. 1935: Hugh Davson and James Danielli suggested the cellular membrane was a sandwich of phospholipids between two layers of hydrophilic proteins. Although the heads of phospholipids are hydrophilic, the surface of a membrane consisting of a pure phospholipid bilayer adheres less strongly to water that does the surface of a biological membrane. By the 1960s, the Davson-Danielli sandwich had become widely accepted as the structure of all of a cells membranes. However, not all cellular membranes are identical and membrane proteins are actually amphipathic. 7. 1972: S. J. Singer and G. Nicolson proposed that membrane proteins are dispersed, individually inserted into the phospholipid bilayer with their hydrophilic regions protruding. 8. A method of preparing cells from electron microscopy called freeze-fracture has demonstrated visually that proteins are indeed embedded in the phospholipid bilayer of the membrane. Freeze-fracture splits a membrane along the middle of the phospholipid bilayer, somewhat like pulling apart a chunky peanut butter sandwich. 9. Most of the lipids and some of the proteins can shift about laterally, but it is quite rare for a molecule to flip-flop transversely across the membrane, switching from one phospholipid layer to the other. 10. A membrane remains fluid as temperature decreases until finally the phospholipids settle into a closely packed arrangement and the membrane solidifies. The temperature at which a membrane solidifies depends on the types of lipids it is made of. The membrane remains fluid to a lower temperature it is rich in phospholipids with unsaturated hydrocarbon tails. 1. The steroid cholesterol, which is wedged between phospholipid molecules in the plasma membranes of animal cells, has different effects on membrane fluidity at different temperatures. At relatively high temperatures (like 37 ºC, the body temperature of humans), cholesterol makes the membrane less fluid by restraining phospholipid movement. However, because cholesterol also hinders the close packing of phospholipids, it lowers the temperature required for the membrane to solidify. 2. Membranes must be fluid to work properly. 11. A membrane is a collage of different proteins embedded in the fluid matrix of the lipid bilayer. Proteins determin most of the membrane’s function. 1. Integral proteins penetrate the hydrophobic core of the lipid bilayer. Many are transmembrane proteins which span the membrane. Other integral proteins extend only partway into the hydrophobic core. The hydrophobic regions of an integral protein consist of one or more stretches of nonpolar amino acids, usually coiled into α helices. 2. Peripheral proteins are not embedded in the lipid bilayer at all; they are appendages loosely bound to the surface of the membrane, often to exposed parts of integral proteins. 3. There are six major functions performed by proteins of the plasma membrane. 1. Transport: A protein that spans the membrane my provide a hydrophilic channel across the membrane that selected for a particular solute. Other transport proteins shuttle a substance from one side to the other by changing shape. 2. Enzymatic activity: a protein built into the membrane may be an enzyme with its active site exposed to substances in the adjacent solution. In some cases, several enzymes in a membrane are organized as a team that carries out sequential steps of a metabolic pathway. 3. Signal transduction: A membrane protein (receptor) may have a binding site with a specific shape that fits the shape of a chemical messenger, such as a hormone. The external messenger may cause a shape in the protein the relays the message to the inside of the cell. 4. Cell-cell recognition: Some glycoproteins serve as identification tags that specifically recognized by membrane proteins of other cells. Cells recognize other cells by binding to surface molecules, often carbohydrates, on the plasma surface. Some membrane carbohydrates are covalently bonded to lipids (glycolipids). Most are covalently bonded to proteins (glycoproteins). 5. Intercellular joining: Membrane proteins of adjacent cells may hook together in various kinds of junctions, such as gap junctions or tight junctions. 6. Attachment to the cytoskeleton and extracellular matrix: Microfilaments or other elements of the cytoskeleton may be non-covalently bound to membrane proteins, a function that helps maintain cell shape stabilizes the location of certain membrane proteins. Proteins that can bind to ECM molecules can coordinate extracellular and intracellular changes. 12. Membranes have distinct inside and outside faces. The asymmetrical arrangement of proteins, lipids, and their associated carbohydrates in the plasma membrane is determined as the membrane is built by the ER and Golgi apparatus. 2. Membrane structure results in selective permeability 1. The biological membrane has the ability to regulate transport across cellular boundaries, a function essential to the cell’s existence. 2. Cell membranes are selectively permeable, and substances do not cross the barrier indiscriminately. 3. Nonpolar molecules, such as hydrocarbons, carbon dioxide, and oxygen, are hydrophobic and can therefore dissolve in the lipid bilayer of the membrane and cross it easily, without the aid of membrane proteins. 4. Polar molecules such as glucose and other sugars pass only slowly through a lipid bilayer, and even water, an extremely small polar molecule, does not cross very rapidly. These hydrophilic substances can avoid contact with the lipid bilayer by passing through transport proteins that span the membrane. 1. Some transport proteins, called channel proteins, function by having a hydrophilic channel that certain molecules or atomic ions use as a tunnel through the membrane. (Water passes through channels called aquaporins). 2. Other transport proteins, called carrier proteins, hold onto their passengers and change shape in a way that shuttles them across the membrane. 3. A transport protein is specific for the substance it translocates, allowing only a certain substance to cross the membrane. Shulin Ye pg 1 of 2 08/31/09 07:28:04 PM  Chapter 7: Membrane structure and function Diffusion: the movement of 3. Passive transport is diffusion of a substance across a membrane with no energy investment molecules of any substance so that 1. The diffusion of a substance across a biological membrane is called passive transport because the cell does not have to they spread out evenly into the expend energy to make it happen. available space 2. Osmosis: The diffusion of water across a selectively permeable membrane. Concentration gradient: The region 3. Tonicity: The ability of a solution to cause a cell to gain to lose water. along which the density of a chemical 1. If a cell without a wall is immersed in an environment that is isotonic to the cell, there will be no net movement substance decreases. No work must of water across the plasma membrane. be done in order to make this happen. 2. If it is immersed in a solution that is hypertonic to the cell, the cell will lose water to its environment, shrivel, Each substance diffuses down its and probably die. own concentration gradient, unaffected by the concentration 3. If it is immersed in a solution that is hypotonic to the cell, water will enter the cell faster than it leaves, and the cell will swell and lyse like an overfilled water balloon. differences of other substances. 4. A cell without rigid walls can tolerate neither excessive uptake nor excessive lose of water. Osmoregulation: the control of water balance. 5. However, the relatively inelastic cell wall will expand only so much before it exerts a back pressure on the cell that opposes further water uptake. At this point, the cell is turgid, which is the healthy state for most plant cells. If a plant’s cells and their surroundings are isotonic, there is no net tendency for water to enter, and the cells become flaccid (limp). 6. In a hypertonic environment, a plant cell will lose water to its surroundings and shrink. Its plasma membrane will pull away from the cell wall (plasmolysis), and the plant will wilt. 4. Many polar molecules and ions impeded by the lipid bilayer of the membrane diffuse passively with the help of transport proteins that span the membrane. This phenomenon is called facilitated diffusion. 1. Channel proteins simply provide corridors that allow a specific molecule or ion to cross the membrane. 2. A group of channel proteins are ion proteins, many of which function as gated channels, which open or close in response to a stimulus. 3. Carrier proteins seem to undergo a subtle change in shape that somehow translocates the solute-binding site across the membrane. 4. In certain inherited diseases, specific transport systems are either defective or missing altogether. 5. Despite the help of transport proteins, facilitated diffusion is considered passive transport because the solute is moving down its concentration gradient. 4. Active transport uses energy to move solutes against their gradients. 1. Some transport proteins can move solutes against their concentration gradients., across the plasma membrane from the side where they are less concentrated to the side where they are more concentrated. 2. To pump a molecule across a membrane against its gradient requires work; the cell must expend energy. Therefore, this type of membrane traffic is called active transport. As in other types of cellular work, ATP supplies the energy for most active transport. 3. Active transport enables a cell to maintain internal concentrations of small molecules that differ from concentrations in its environment. 1. One transport system that works this way is the sodium-potassium pump, which exchanges sodium for potassium across the plasma membrane of animal cells. Membrane potential: the voltage 4. The cytoplasm is negative in charge relative to the extracellular fluid because of an unequal distribution of anions and across a membrane (ranges between cations on opposite sides of the membrane. Thus, two forces drive the diffusion of ions across a membrane: a chemical -50 to -200 mV). force (the ion’s concentration gradient) and a electrical force (the effect of the membrane potential on the ion’s movement.) This combination of forces action on an ion is called electrochemical gradient. 1. A transport protein that generates voltage across a membrane is called an electrogenic pump. The sodium- potassium pump seems to be the major electrogenic pump of animal cells. The name electrogenic pump of plants, fungi, and bacteria is a proton pump, which actively transports hydrogen ions (protons) out of the cell. 5. A single ATP-powered pump that transports a specific solute can indirectly drive the active transport of several other solutes in a mechanism called cotransport. A plant cell uses the gradient of hydrogen ions generated by its proton pumps to drive the active transport of amino acids, sugars, and several other nutrients into the cell. 5. Bulk transport across the plasma membrane occurs by exocytosis and endocytosis. 1. Large molecules, such as proteins and polysaccharides, as well as larger particles, generally cross the membrane in bulk be mechanism that involve packaging vesicles. Like active transport, these processes require energy. 2. The cell secretes certain biological molecules by the fusion of vesicles with the plasma membrane (exocytosis). 1. Many secretory cells use exocytosis to export products. 3. In endocytosis, the cell takes in biological molecules and particulate matter by forming new vesicles from the plasma membrane. Although the proteins involved in the processes are different, the events of endocytosis looks like the reverse of exocytosis. There are three types of endocytosis: 1. Phagocytosis: Cellular eating. 2. Pinocytosis: Cellular drinking. 3. Receptor-mediated endocytosis: Human cells use receptor-mediated endocytosis to take cholesterol for use in Ligand: any molecule that binds the synthesis of membranes and other steroids. Cholesterol travels in the blood in particles called low-density specifically to a receptor site of lipoproteins (LDLs), complexes of lipids and proteins. LDLs act as ligands by binding to LDL receptors on an