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Plopper Cell Biology Chapter 1

by: Taylor Swifty

Plopper Cell Biology Chapter 1 BIOLOGY 202

Marketplace > University of Missouri - Kansas City > Biology > BIOLOGY 202 > Plopper Cell Biology Chapter 1
Taylor Swifty
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These notes cover Chapter 1 from Principles of Cell Biology by Plopper.
Cell Biology
Edward Gogol
Class Notes
Cell, Biology, Chapter, 1, Plopper
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This 23 page Class Notes was uploaded by Taylor Swifty on Monday September 5, 2016. The Class Notes belongs to BIOLOGY 202 at University of Missouri - Kansas City taught by Edward Gogol in Fall 2016. Since its upload, it has received 42 views. For similar materials see Cell Biology in Biology at University of Missouri - Kansas City.


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Date Created: 09/05/16
Chapter 1 What is a Cell? 1.1 – The Big Picture First 4 chapters  “What are cells made of?” Last 10 chapters  10 Principles of Cell Biology This chapter is organized into 5 sections: 1) Provides an overall intro to the fundamentals of cell bio including basic chem that helps define how cells are built & function and focuses on structural organization of simplest of 4 cellular building blocks: sugars. 2) overview of the common structures we will encounter in more detail in later chapters. First Section - The Cell Is the Fundamental Unit of Life  introduction to some essential concepts that form foundation for supporting life.  includes the definition of life as well as an examination of the three domains of living organisms  introduces the concept that evolution by natural selection takes place at even most basic levels of living organisms. Second Section - An Overview of the Molecular Building Blocks of Cellular Structures  introduces some of the basic chem that governs how molecules in living organisms interact.  lists some of the most common chemical structures found in biomolecules which form a critical part of the structure–function relationship  This section is also where we take our closest look at sugars.  How they are used to synthesize nucleotides, another class of cellular building blocks.  Pay particular attention to how sugars are assembled into polymers, as we will be referring to these polymers in several chapters. Third section - Cells Contain Distinct Structures That Perform Specialized Functions  focuses on the structures in eukaryotic cells called organelles  these organelles are multitaskers, so most will appear in several chapters.  Many students are tempted to map an organelle to one or two specific cellular functions (e.g., nucleus = DNA replication), when in fact every organelle can perform many functions at the same time. o Thus, when we discuss DNA packing, DNA replication, nuclear pore transport, and regulation of gene expression  these events are all occurring simultaneously in the nucleus, and they often influence one another. Fourthsection -Cells in Multicellular Organisms CanBeHighlySpecializedto PerformaSubset of theFunctions Necessary for Life  take a quick look at the structure and function of tissues, the next highest order (after cells) of biological organization. Fifth section - Model Organisms Are Often Studied to Understand More Complex Organisms  explains where most of the information we will examine in later chapters comes from.  While we will not be examining any of these organisms in detail in this book, it is important to recognize that at the cellular level, seemingly different organisms (such as bacteria, plants, flies, worms, and fish) share nearly as many similarities with us as does the familiar lab mouse, because they are all built on the same principles we will discuss in this book. 1.2 – The Cell Is the Fundamental Unit of Life Cell biologist’s definition of life = a chemical system capable of Darwinian evolution So things that are alive:  must have ability to generate exact copies of themselves and self-correct (i.e. restore themselves to defined state by repairing damage)  no chemical reaction is able to do both replication and repair So by the above definition  proteins and DNA are not alive, as well as enzymes (even though they can catalyze many reactions) even if they exist inside an organism because they lack one or both of these abilities. Life  trait possessed only by groups of molecules that work together Biologists believe earliest biological molecules may have been simple molecules that could self-replicate  these molecules were then enclosed in a selective barrier, called a membrane, after which they were capable of forming teams that cooperated to maintain a fairly constant internal environment, even when conditions outside membrane varied greatly  Molecular teams that developed additional ability to repair or replace damaged team members were then able to generate nearly exact replicas of themselves, including the membrane. This membrane-enclosed team of molecules is now called a cell. Membrane  is often referred to as the plasma membrane or cell membrane  it encloses a compartment called the cytosol or cytoplasm. All living beings are composed of cells – fundamenal unit of life.  simplest cells are called prokaryotes, to distinguish them from more complex cells known as eukaryotes. Cells Are Self-Replicating Structures That Are Capable of Responding to Changes in Their Environment Teamwork:  Division of labor is a common theme in cell bio  No single molecule can both self-replicate and self-maintain  These tasks are tackled by cooperating groups of molecules that specialize in specific activities. Cells contain molecular teams responsible for these essential tasks:  Maintain internal environment o Living organisms capture and store energy by forming and maintaining chemical disequilibrium with external environment. o To remain alive, cells must continually adjust internal activities to maintain a consistent environment that differs from conditions outside cell membrane.  Sensing the external environment o cells have to be “aware” of changes in ext environment that may impact their own int environment (e.g., temp, pH, nutrient levels,osm). o cells contain sensors for relevant environmental conditions such as these  Controlling the flow of molecules into and out of the cell o cells communicate with their ext environment mainly through selective transport of molecules (e.g., let in nutrients and push out metabolic waste) o controlling this traffic helps cells maintain chemical disequilibrium and sense surroundings.  Catalyzing chemical reactions o In order to maintain consistent int environment, cells must be able to control chem reactions taking place w/in them. o Enzymes play an important role in regulating these reactions.  Generating useful energy o to catalyze most chem reactions and do any form of work, cells must expend energy. o many molecules in cells are devoted to capturing energy from outside cell (e.g., photosynthesis - sunlight and “food”) and converting it into small number of energy forms that cells use directly. o A well-known example of a useful energy form is adenosine triphosphate (ATP)  Storing genetic information o cells contain instructions for manufacturing most of bio molecules necessary to stay alive. o These instructions are stored in DNA, a simple molecular polymer.  Synthesis of biological molecules o A considerable amount of captured cell energy is used to construct new biological molecules inside cells.  These molecules may replace damaged molecules, permit new functions in the cell, or generate sufficient copies of a molecule for cell to replicate.  To generate a nearly exact copy of itself, cell must ensure all info. stored in its DNA is present in newly created daughter cell.  Cells possess molecular teams responsible for accurately replicating DNA & properly segregating it during cell division.  Regulating information flow o Molecular teams in a cell communicate with each other - some molecules specialize in transferring info. from one team to another. Prokaryotes Are the Simplest Form of Cells All organisms are classified into one of three domains:  Bacteria (Prokaryotes)  Archaea (Prokaryotes)  Eukarya (Eukaryotes) Prokaryotes:  Have only one membrane - the plasma membrane o all of their internal chem reactions take place in the cytosol  so degree of specialization that these cells can achieve is limited. o Some prokaryotes have elaborate changes of the plasma membrane, such as stacks of membrane folds that provide some degree of compartmentalization. o The cytosol of prokaryotes appears heterogeneous when viewed with EM, suggesting that it may be partially organized.  Are unicellular o do not assemble into multicellular organisms, although some cluster to form biofilms  Do not divide by mitosis o Most genetic information in prokaryotes is contained in single circular DNA molecule called a chromosome, while eukaryotic cells contain several chromosomes. o Mitosis, an elaborate mechanism to ensure proper segregation of chromosomes during cell division, is in eukaryotic organisms only. Archaea  classified as distinct prokaryotes because they differ in four important ways from bacteria. st o 1 - the enzyme complex they use to synthesize RNA is more similar to the eukaryote complex tndn the bacterial one. o 2 - the protein and RNA components of ribosomes in archaea are more similar to those found in eukaryotes. o 3 - the cell membranes of archaea contain components not found in bacteria or eukaryotes. o 4 - the components of the cell walls in archaea are also quite different from bacteria. Prokaryotes  can occupy some of harshest environments on earth - extreme heat and cold, tremendous P atm, little or no atmospheric oxygen, and pH values ranging from 2 to 12.  Why? Likely because modern prokaryotes are direct descendents of Earth’s earliest cells, which are estimated to have 1st appeared about 3.5 billion years ago, when Earth’s atmosphere was much different from today.  Because they’re highly adaptable, prokaryotes are by far the most abundant organisms on Earth. Prokaryotic Cells Are Protected by a Cell Wall Prokaryotes  most, if not all, have an additional layer of protection outside plasma membrane = cell wall  portion of cell wall that is directly connected to plasma membrane is often called the capsule. Cell wall  is composed largely of sugar molecules linked together to form thick mesh.  provides protection against physical trauma  retains water to help ensure cell is properly hydrated. Eukaryotes Are Complex Cells Capable of Forming Multicellular Organisms Eukaryotic cells  comprise the third, and most recent, domain of biological organisms  when viewed under microscope, the most striking feature is the cytosol is highly organized.  presence of a large, often oval-shaped nucleus o the presence of a nucleus is the defining feature of eukaryotic cells. Closer examination with more powerful microscopes allows us to see additional distinct structures in the cytosol  classified into two groups:  Organelles - cytosolic structures that are surrounded by at least one distinct membrane o The presence of these membranes allows cell to create specialized compartments in cytosol that are devoted to performing subset of cellular tasks under optimized conditions. o Like plasma membrane, these membranes are selectively permeable, which helps to create a unique internal environment optimally suited to molecules contained inside. o Examples: nucleus, endoplasmic reticulum, Golgi apparatus, mitochondria, chloroplasts, endosomes, lysosomes, and peroxisomes.  Each of these organelles contains unique molecules and performs a separate set of functions.  Large molecular complexes that are not enclosed in a separate membrane do not have a generic name o they do share one important trait: they represent specialized regions in cytosol that are devoted to a subset of cellular tasks.  For example, eukaryotic cells contain three different types of fibers that serve as scaffold for organization of cytosol = cytoskeleton.  Careful arrangement of the cytoskeleton is essential for proper cell function  without it, muscle cells would not contract; nerve cells would fall silent. Some Eukaryotic Cells Contain Structures That Allow Them to Form Multicellular Clusters  High degree of compartmentalization  can customize cytosol to generate a tremendous # of different cell types.  ~1 billion years after cells first appeared, some eukaryotic cells acquired ability to work together in groups  multicellular organisms. o Structural basis for multicellularity is revealed by a small number of structures that hold adjacent cells together, many of which are also linked to cytoskeleton o This creates a supercytoskeleton that spans multiple cells, helps integrate them into a single functioning unit. 1.3 – An Overview of the Molecular Building Blocks of Cellular Structures Structure-Function relationship = the function of any biological entity can be determined by understanding its underlying structure Water Is the Most Common Compound Found in Cells All living cells contain water  It’s likely that first chemical reactions to form that cell occurred in water 5 Aspects of Water  Exists as liquid at room temperature and normal atmospheric pressure (compounds that are of similar mass to water, like methane and ammonia, are gases at room temp and norm atmospheric pressure)  Very polar molecule – high electronegativity of oxygen causes hydrogen electron in covalent bond to spend majority of time circling nucleus of oxygen, resulting in imbalance of charge --- Oxygen partially negative δ-, Hydrogen partially positive δ+. That imbalance holds water molecules together since partially negative charge of oxygen attracts partially negative hydrogen from OTHER water molecules = hydrogen bonding  Liquid phase has higher density than solid phase under standard conditions – which is why ice floats in water – hydrogen bonding packs molecules closer together than regular repeating arrangements found in crystals. If liquid water forms ice in cells, the increased volume of solid water can tear membranes and rupture cells.  Extensive H bonding in water allows it to absorb a great deal of heat before it changes temperature. 1 calorie of heat is required to heat 1 mL of water by 1 degree Celsius = specific heat. The specific heat for water is higher than for other liquids. So that means that water can serve as a great insulator against heat generated by chemical reactions in a cell  High polarity of water  takes a relatively large amount of heat to vaporize liquid water = heat of vaporization. Examples: Sweating = which is water as a coolant and Transpiration in plants = transport molecules The Chemical Properties of Water Impact Nearly All Molecular Interactions in Cells Understanding water helps us understand how molecules behave inside of cells. Water is polar  so if a molecule is compatible with it, it’s hydrophilic, if it’s incompatible with it, it’s hydrophobic.  Hydrophilic mol+cule+ − o ions (H , Na , Cl , etc.), other polar molecules (e.g., sugars, ammonia) o the charge imbalance attracts the polar atoms in water.  Hydrophobic molecules o nonpolar (and contain no charged atoms) o no charge imbalance therefore, they do not attract water (oil immersed in water --- oil doesn’t disperse but clusters together in a layer to avoid contact with water) Cells can benefit from having hydrophobic molecules. 3 major advantages that hydrophobic molecules offer cells: 1. Hydrophobic molecules spontaneously cluster together in water. a. This principle is underlying reason whyphospholipids, which form bulk of biological membranes, spontaneously assemble into a bilayer when submerged in water. b. the fatty acid tails in phospholipids are hydrophobic and thus cluster together naturally. Cells have to expend little or no energy to organize phospholipids into a membrane. 2. A second advantage is this spontaneous assembly process permits membranes to automatically reseal if they are punctured (self-maintenance is a critical feature of all cells). 3. A membrane composed of hydrophobic molecules repels most hydrophilic molecules, creating an effective barrier to hydrophilic molecules between two sides of that membrane  main reason why cells can create their own internal environment. Advantages of water’s H bonding to other hydrophilic molecules:  polar (and ionic) molecules dissolve readily in water  cells can concentrate a large # of them on one side of a membrane  As we will see in later chapters, the concentration and movement of ions across membranes is a common activity in all cells, and is responsible for conducting electrical signals in our nervous system. The Study of Cellular Chemistry Begins with an Examination of the Carbon Atom Carbon is important for three reasons in cells:  carbon-containing compounds are most abundant molecules in cells (except water)  these compounds exist in an array of variations - of all known molecules, those containing carbon vastly outnumber all the rest (w/o carbon), combined.  carbon atoms can attach to one another more readily than atoms of any other element, giving rise to molecules of tremendous size (some contain several thousand carbons) and structural complexity. Carbon Forms Characteristic Bonds with Hydrogen, Oxygen, Nitrogen, and Other Carbons  The number of carbon-containing compounds is so vast that they are classified into groups (or families) according to their structure.  Despite their tremendous complexity, C-containing compounds are typically constructed from a small number of basic chemical shapes.  In cells, C atoms are typically covalently bound to only four other atoms: H, O, N, and other Cs.  Most carbon-based compounds in cells are built with these simple structures. Carbon  contains six electrons, arranged in three orbital configurations. o Two electrons are present in 1s orbital (the innermost shell), filling it. o The other four electrons are located in second (valence, or outermost) shell  two are in the 2s orbital, and in a single (unbound) carbon atom  other two are unpaired and occupy two of the three 2p orbitals.  when binds to four other atoms, these four bonds are arranged in a tetrahedral pattern, with bond angles of 109.5°  when binds to three other atoms, one of these atoms forms a double bond, and this forces the other two atoms into a trigonal, planar configuration  when binds to two other atoms, the three atoms adopt a linear arrangement  can be connected to two atoms by a pair of double bonds (e.g., carbon dioxide) or by a triple bond and a single bond (e.g., cyanide).  does not form four covalent bonds with a single atom. Octet rule states that nonmetallic atoms tend to gain, lose, or share electrons until they are surrounded by eight valence electrons.  Because carbon has only four electrons in its valence shell, it “needs” four additional electrons. o It fills the remaining positions in the two 2p orbitals by forming four covalent bonds with other atoms  results in rearrangement of the valence shell, as shown: one electron in the 2s shell is “borrowed” by the 2p orbitals, resulting in the formation of four orbitals called sp hybrids. o These four bonds adopt characteristic shapes for each configuration Complex Biomolecules Are Mostly Composed of Chemical Building Blocks Called Functional Groups Carbon always binds to at least two other atoms, these atoms and their associated binding partners can be easily combined to create a wide variety of structures. The field of organic chemistry  is devoted to the study of chemical compounds in organisms, subdivides them according to their chemical structure.  The different classes are called functional groups o while not all functional groups contain carbon, those that do are by far the most abundant in cells. Lipids Are Carbon-Rich Polymers That Are Insoluble in Water When carbon forms covalent bonds with O or 2 2:  these bonds are classified as polar (oxygen and nitrogen are more electronegative than carbon). When carbon forms covalent bonds with C or H:  C–C bonds are nonpolar  C–H have so little polarity that most molecules consisting only of carbon and hydrogen do not attract water (hydrocarbons)  hydrophobic and do not dissolve in water. Lipids  are a class of hydrocarbons commonly found in cells  are insoluble in the cytosol  most lipids in cells are modified and thus attached to hydrophilic functional groups that confer some degree of water solubility  amphipathic (“having both properties”). Common modified lipids include:  Phospholipids  most common form of modified lipids in cells o constitute most of the mass of cellular membranes  Cholesterol o is an essential component of cellular membranes. o is largely hydrophobic o is most commonly found in the middle (hydrophobic) zone of membranes, where it interacts with phospholipids to change mechanical properties of membrane o In some animals, derivatives of cholesterol used as hormones that circulate in body to permit communication between even very distant cells.  Triglyceride o commonly known as fat o serve as an important form of energy storage in animals o largely insoluble in water  form distinct droplets o are transported through the circulatory system, bound to proteins to form a lipoprotein. o Some lipids are permanently attached to proteins, where they play an important role in targeting these proteins for cell membranes  sometimes referred to as lipid tails, and they serve as a form of anchor by interacting with hydrophobic region of the membrane to keep the protein in place. Sugars Are Simple Carbohydrates Carbohydrates  are composed entirely of carbon, hydrogen, and oxygen  often, these atoms are present in a ratio ofnC2nOn  Chemists speculated that they might be arranged such that carbon atoms are attached to water molecules (hydrates), and so they referred to them as carbohydrates (we now know that this is not the arrangement of these compounds, but the name stuck).  typically form rings or linear strands of linked carbon atoms  the oxygen and hydrogen atoms are present in functional groups (with names such as hydroxyls, carbonyls, aldehydes, alkanes, etc.) formed by the carbons. Sugars  are common carbohydrates found in cells  All contain at least three carbons  one carbon forms a carbonyl group, which exists as either an aldehyde or a ketone; the remainder of the carbons are attached to hydroxyl groups  The most important sugars in cell metabolism contain btw three and seven carbons. The Common Sugars Glucose and Ribose Serve Several Different Functions in Cells Sugar has an important role as a source of metabolic energy but it’s more than just food.  Ribose (five C sugar) and Deoxyribose form the backbone of RNA and DNA (nucleic acids), respectively  Glucose (six C sugar) – serves as building block for complex molecules such as starch, cellulose (a major component of the cell wall in plants), and chitin (found in exoskeleton of arthropods). Many Sugars Exist as Disaccharides in Cells Monosaccharides (simplest form of a sugar)  Glucose and ribose are examples of the simplest form of a sugar Disaccharides (linked pairs)  Commonly found in cells  Examples: o Common table sugar (sucrose) = glucose and fructose (6 carbon sugar) o Lactose and maltose are other common disaccharides.  Two important properties help determine their function in cells. o The first of these is simply the types of monosaccharides they contain. o The second is how they are connected  All monosaccharides are linked by a glycosidic bond (an ether bond specific to sugars) between the carbon atoms on each sugar, but these bonds are not all the same.  All disaccharides are formed between sugars in a ring form.  The two sides of the ring are never identical, because each carbon in the ring has two different atoms (−H, −OH, or −CHO) projecting outward.  This means that the bond formed between two carbons oriented in same direction is different from the bond that joins two carbons facing in opposite directions, even if same carbons are involved.  Each carbon in a monosaccharide is assigned a number, followed by an apostrophe to designate the term “prime” (1′: one prime, 2′: two prime, 3′: three prime, etc.)  The bond between carbons in two monosaccharides is identified by simply listing the involved carbons, separated by a comma (e.g., 1′, 4′).  These bonds are classified as either α or β according to the specific orientation of the 1′ carbon. Notice, for example, the α and β orientations of glucose. o A seemingly minor point such as the orientation of a single atom has profound effects for cells. All of the chemical reactions necessary to make and break bonds between sugars:  are catalyzed by enzymes, which are proteins that contain a binding site where these chemical reactions take place. o Each enzyme has its own specific binding site  this means that an enzyme that catalyzes formation of an α-1,4 glycosidic bond cannot also catalyze formation of an α-1,6 bond or a β-1,4 bond because these bonds are shaped differently.  enzymes that degrade a specific bond cannot degrade others o Practically speaking, this difference determines which disaccharides cells can make and degrade, based type of enzymes they contain. o also explains why humans can digest many α-1,4 bonds (e.g., in sucrose and maltose) but not most β-1,4 bonds (e.g., in chitin and cellulobiose) – (vegetable products end up in your crap) o human cells contain few enzymes capable of binding and breaking β1,4 glycosidic bonds. The enzyme lactase, which breaks the β1,4 bond in the disaccharide lactose, is expressed only in infancy in most mammals. Oligosaccharides and Polysaccharides: The Storage, Structural, and Signaling Components of Cells Cells can build monosaccharides  disaccharides  polysaccharides (large polymers)  complex branching structures (two different types of these complexes: oligosaccharides and polysaccharides) Oligosaccharide (“oligo-” means many)  sugars attached to cellular proteins and lipids  play an important role in determining shape and function of molecules they are attached to. Polysaccharides (“poly-” means even more than oligo)  tremendously large complexes of sugar that lie outside of cells in the extracellular space.  play a number of different roles in organisms, including long-term storage of food sugars and as a reinforcing material in plant cell walls. In animals, oligos and polys:  are important components of EC matrix = a dense network of molecules that provide structural support to tissues  can contribute to cell signaling networks Amino Acids Form Carbon-Rich Molecules That Contain an Amino Acid Group and a Carboxylic Acid Group Amino acids  are the building blocks of proteins  Each amino acid contains a central carbon atom, called an α-carbon, attached to four different molecular structures. o an amino group o a carboxylic acid group o hydrogen atom o amino acid side chain (or “R” group), differs in each different amino acid.  The proteins in cells are constructed from 20 different amino acids o these 20 amino acids are classified into three groups, according to the chemical nature of the side chains.  Nonpolar  Polar  Ionic Proteins  are composed of long, linear sequences of amino acids. o These sequences are created by forming covalent bonds (peptide bonds) between carboxylic acid group of one amino acid and amino group of another amino acid. o Depending upon the number of amino acids linked together, the names of the polymers differ  two amino acids linked together = dipeptide  three amino acids linked together = tripeptide  polypeptide = polymers of 10 or more amino acids o when polypeptides fold into a stable configuration that is useful to cells, they are called proteins. Chemical Modifications of Amino Acids Help Control Protein Function The structure-function relationship predicts:  any condition that alters shape of a protein  impacts its function. o Changes in a protein’s environment (temperature, pH, ionic strength, etc.) have global effects on protein folding and function  Cells use targeted chemical modifications of individual amino acids to slightly alter protein shape o these modifications are carried out by other proteins, and so are comparatively easy to control o Examples of these modifications: addition of phosphate, methyl, and acetyl groups to the side chains of amino acids.  These modifications are easily reversible, which allows cells to fine-tune the shape of individual proteins w/great precision. o Other modifications are permanent, and essential for protein function.  creation of disulfide bonds between the sulfhydryl groups in cysteine amino acid side chains  addition of oligosaccharides to some asparagine and serine amino acid side chains. Nucleotides Are Complex Structures Containing a Sugar, a Phosphate Group, and a Base Nucleotides  are building blocks for DNA and RNA  the genetic material of cells  in RNA  contain a five-carbon sugar called ribose  in DNA  contain a modified ribose called deoxyribose  sugar portion of nucleotides is always in ring conformation.  One, two, or three phosphates are attached to the 5′ carbon, and a nitrogen-containing base is attached to the 1′ carbon.  Polymers are assembled by joining the 3′ carbon of one nucleotide to the single phosphate attached to the 5′ carbon of another. 1.4 – Cells Contain Distinct Structures That Perform Specialized Functions Cells use a lot of energy to make polymers and devote a lot of effort to assemble them into functional teams, so that they function optimally.  Both prokaryotes and eukaryotes organize cytosolic proteins into clusters  Eukaryotes go a step further by enclosing some of these teams in membranes, thereby creating compartments (organelles). o Compartmentalization is key to understanding cells, as it not only permits cells to delegate related tasks to sub-compartments  also permits entire cells to specialize in a subset of tasks required in a multicellular organism. o Most of the specialized structures occur in eukaryotic cells, we will focus largely on eukaryotes in this book. The Plasma Membrane Is a Semipermeable Barrier between a Cell and the External Environment Plasma membrane  primary function is to permit cells to create a chemical environment distinct from the outside world, in which cells are continuously striving to maintain this internal environment at an optimal set point  homeostasis. o A large part of this is accomplished by hydrophobic portions of membrane phospholipids  serve as a barrier to most hydrophilic molecules. o Preventing passage of molecules through plasma membrane is not enough to ensure homeostasis o Cells must also have way to allow molecules to enter and exit cytosol in a controlled fashion. Proteins in the plasma membrane  control nearly all molecular traffic between cell and external environment  Many of these proteins actually span membrane = transmembrane proteins  Classes of proteins called channels, carriers, and pumps o act as selective passageways that permit transit of ions and small molecules such as sugars and amino acids. o most large molecules entering cell are captured by transmembrane receptor proteins at cell surface  then clustered into a patch on the plasma membrane internalized by endocytosis o Molecules synthesized by cells can be expelled by exocytosis. Protein Complexes in and near the Plasma Membrane Control a Cell’s Attachment to the External Environment and to Other Cells Plasma membrane  2 function of plasma membrane is to provide means for attaching to and interacting w/molecules in external environment (extracellular space). o handled entirely by proteins in or near plasma membrane that form stable complexes w/proteins capable of generating and/or resisting mechanical force. o The bulk of proteins that perform this task are present in cytosol, and bind to the cytoplasmic portion of a specific set of transmembrane receptor proteins. o In multicellular organisms, similar complexes form around different types of transmembrane proteins that act as receptors for neighboring cells. o Both types of protein complexes can associate with the cytoskeleton. The Plasma Membrane Contains a Wide Variety of Proteins That Allow Communication between Cells Plasma Membrane  Permits communication between cells, especially in a multicellular organism, even when separated by a great distance = signaling  Mechanism that cells use to interpret signals is called signal transduction.  Many molecules that act as signals between cells cannot pass through plasma membrane o they are bound by yet another class of transmembrane receptor proteins dedicated to this. o The resulting shape change in receptors induced by binding of signal molecules  triggers other proteins in cytosol to activate  delivering the messages carried by the signal molecules. The Nucleus Is the Central Storehouse of Genetic Information All cells carry with them the info. necessary to synthesize almost every molecule they need to survive.  is encoded in the sequence of nucleotides that make up the DNA molecules, also known as the genome.  these sequences reflect billions of years of evolution and are most valuable material in a cell.  Alteration, damage, or loss of this info. (known as mutation) could permanently injure or even kill a cell.  Cells must protect DNA from any potentially dangerous agents. What is the strategy for protecting DNA? First:  most of a cell’s DNA is enclosed in an organelle (nucleus) committed entirely to its use and maintenance  the nucleus is an organelle surrounded by two membranes (like the mitochondrion and chloroplast, each of which contains its own small genome)  The double membrane surrounding these organelles is an excellent barrier to most insults, and many cell biologists believe that these shared traits reflect a common ancestry: each arose from a cell that was engulfed, but not destroyed, and then developed a symbiotic relationship with its host  endosymbiotic theory. Second:  limit access through use of highly selective portals (nuclear pore complexes) that penetrate nuclear double membrane.  They permit entry into and exit from interior of the nucleus (sometimes called the nucleoplasm) through intricate system of proteins devoted solely to this task. Third:  carefully package it in a form that restricts access to only those portions of the DNA that are currently needed.  strands of DNA are tightly wrapped around a protein scaffold to form a complex called chromatin. o chromatin can be so tightly twisted, it reduces length of a chromosome by approximately 20,000- fold (For an understanding of exactly what this means, consider the effort that would be required to twist a rope 20 km [over 12 miles] long into a structure only 1 meter long.) o By carefully unwinding only those portions necessary at any given time, cells secure structural integrity of chromosomes. Fourth:  cells make RNA copies of DNA sequences (transcription), then use them to assemble machinery necessary for cell function.  This strategy is effective because any mistakes that arise from misreading RNA, damage to RNA, and so on, take place outside nucleus.  With the exception of ribosomes (which are formed by nucleolus, a specialized sub-region in nucleus), all macromolecules other than DNA and RNA are assembled outside nucleus. Chloroplasts Build Food Molecules from CO and H O Using 2ight Ene2gy Chloroplasts:  function of chloroplasts is to harness light energy from sun to create carbon polymers necessary for building all of the other macromolecules in cells.  Only autotrophic cells (literally, cells that nourish themselves), such as those found in the leaves of plants, contain chloroplasts.  The biochemical steps required are numerous and organized into two classes. o The first, sometimes called the light reactions  concerned with capturing photons of light and using this energy to strip electrons from water molecules and add them to carbon dioxide (CO) m2lecules  results in the release of molecular oxygen (O2 and the accumulation of two types of three-carbon sugars: glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. o The second (dark reactions)  is concerned with converting these sugars into starch and sucrose.  In turn, these provide the necessary molecules for building all of the other biomolecules necessary for cell function.  capitalize on selective permeability of membranes to build molecular gradients across them as form of intermediate energy storage. o Many of these are ion gradients, built by ion pump proteins. o The PE stored in these gradients can later be used by membrane proteins to drive energy- dependent chemical reactions, such as synthesis of ATP from ADP and inorganic phosphate that occurs in chloroplasts and mitochondria. Mitochondria Convert Food to Cellular Energy Chloroplasts  committed to creation of many complex biomolecules Mitochondria  committed to dismantling and breaking down complex biomolecules, in a way that allows them to harness as much released energy as possible, and has numerous biochemical steps (just like in chloroplasts) o The first is concerned with stripping high-energy electrons off of food molecules and storing them in a set of molecules designated as high-energy electron carriers. o In second set of reactions, these electrons are combined with protons and molecular oxygen to create H2O  during this process, the energy of electrons is temporarily stored as proton gradient across inner membrane of mitochondria  used to generate ATP. The Endoplasmic Reticulum and Golgi Apparatus Collaborate to Modify, Sort, and Transport Proteins and Phospholipids to Their Final Destinations An excellent example of teamwork in cells:  way in which the endoplasmic reticulum (ER) and Golgi apparatus work together to handle much of membrane trafficking that takes place inside cells. The Endoplasmic Reticulum Is Composed of the Smooth Endoplasmic Reticulum and the Rough Endoplasmic Reticulum The membrane defining the endoplasmic reticulum is attached to the outer membrane of the nucleus and forms two distinct structures that perform different functions. Smooth Endoplasmic Reticulum (smooth ER) is specialized to perform 4 important functions:  is the site of phospholipid biosynthesis. o Phospholipids are synthesized on the cytoplasmic face of the SER membrane, and then distributed to the rest of the cell membranes.  serves as a storage site for calcium ions. These ions are released in brief bursts to control the activities of calcium-dependent proteins, and then quickly pumped back into the SER to shut these proteins off.  In some cells, such as liver and muscle cells, proteins associated with the SER membrane play an important role in converting stored energy (in the form of glycogen, a polymer of glucose held together by α-1,4 bonds) into individual glucose molecules for immediate use by cells.  The SER also contains enzymes that inactivate biochemical toxins; these are found in great abundance in liver cells, which remove these toxins from the bloodstream. Rough Endoplasmic Reticulum (rough ER)  is responsible for controlling synthesis, modification, and assembly of two important classes of cellular proteins.  can be easily distinguished from SER by presence of numerous ribosomes, which dot cytoplasmic surface of the RER, giving it a comparatively “rough” appearance, under EM o Ribosomes attached to the surface of the RER are actively synthesizing polypeptides that pass from the cytosol through a complex of membrane proteins called the translocon and into the interior, or lumen, of the RER.  Many of these polypeptides do not pass entirely into the lumen, because they contain one or more regions of hydrophobic amino acids that remain in the RER membrane. Polypeptides like these that have one or more transmembrane sequences form transmembrane proteins, the first class of proteins. The second class of polypeptides synthesized by ribosomes on the RER consists of those that pass entirely through the translocon without attaching to the RER membrane. A generic term for proteins synthesized in this fashion is soluble proteins; a subset of these are ultimately released into the extracellular space, and are therefore called secreted (or secretory) proteins. Proteins synthesized by ribosomes of the RER:  undergo a series of chemical modifications (post-translational modifications) catalyzed by enzymes in RER. o The most striking of these modifications is the addition of branched oligosaccharides to some asparagine and serine side chains, a process known as glycosylation.  As discussed previously, these oligosaccharides play an important role in controlling the structure and function of the proteins they are attached to. o A second type of modification is the formation of a covalent bond between the sulfur atoms in two cysteine amino acid side chains, called a disulfide bond.  Because it is covalent, it is very difficult to break and essentially locks the two cysteines together, which helps stabilize protein structure. o Some proteins receive a third form of modification, the addition of a phospholipid to the carboxyl terminus of the polypeptide, which anchors the protein to the luminal face of the endoplasmic reticulum membrane. Traffic between the RER and Golgi Apparatus Is Carried by Membrane-Bounded Vesicles With the exception of proteins destined to remain in RER to assist with translocation and modification of newly synthesized polypeptides (often called ER-resident proteins), all other polypeptides synthesized by RER- associated ribosomes are carried to Golgi apparatus.  The mechanism cells use to accomplish this is quite complex, only partially understood.  With the assistance of proteins designated specifically for the task, small patches of the RER membrane pinch off to form a small, membrane-bound compartment called a vesicle (which contains both transmembrane proteins and soluble proteins) o This vesicle  Golgi apparatus by motor proteins associated w/cytoskeleton, and a different set of proteins assist in fusion of vesicle with the Golgi membrane. o Similar mechanisms used to shuttle vesicles from Golgi  RER and between different compartments in the Golgi. o Transportation of vesicles between organelles is called membrane trafficking. The Golgi Apparatus Modifies and Sorts Proteins Destined for the Plasma Membrane and Lysosomes The Golgi apparatus  is the only organelle with a defined cellular orientation (i.e., a “front” and a “back”)  consists of a single membrane-bounded compartment that is highly folded to generate separate compartments (cisternae)  vesicles arriving from RER  fuse with cis-Golgi network (CGN) o CGN-resident proteins further modify newly arrived proteins by adding and subtracting sugars to/from their oligosaccharides. o Post-translational modifications continue as proteins are carried by more vesicles  the medial Golgi stacks  trans-Golgi network (TGN) trans-Golgi network (TGN)  one of most important functions of TGN – sort membrane and soluble proteins into vesicles specifically targeted to other organelles or to the plasma membrane o Example: while many of the mechanisms responsible for this sorting are not well known, one very clear case concerns targeting of proteins to the lysosome.  In mammalian cells, one set of modifications to protein-linked oligosaccharides results in formation of a sugar called mannose 6-phosphate (or M6P).  A protein in the TGN called the mannose 6-phosphate receptor binds to any protein bearing an M6P tag and directs it into a vesicle destined for the lysosome.  Other vesicles budding from TGN are targeted to plasma membrane  The process of synthesizing proteins in RER  shuttling them through different compartments of the Golgi  sending them to plasma membrane is called exocytosis.  soluble proteins that are exocytosed are released into extracell space  membrane proteins that reach plasma membrane via this route remain associated with it after vesicle fusion  how cell surface proteins are delivered to plasma membrane. The Endosome Sorts and Condenses the Contents of Endocytic Vesicles  The formation of vesicles (endocytic vesicles) at plasma membrane usually occurs after cell surface receptors have bound to their ligands and clustered into a patch = receptor-mediated endocytosis  The contents of endocytic vesicles undergo sorting in an organelle called the endosome. Endosomes  Inside the endosome: o ligands detach from their receptors o some of the cell surface receptors are sorted into a vesicle that returns them to the plasma membrane for reuse.  Vesicles from TGN bearing M6P receptors and their cargo also fuse with endosomes  dissociation of the M6P receptors and M6P-tagged proteins.  sort the M6P receptors into a vesicle that returns them to the TGN so they can be reused. Sorting by endosomes  mechanisms responsible for this sorting is not well understood  clear that acidification of the endosome lumen plays an important role  Some of the M6P-tagged proteins arising from the TGN are proton pumps, that pump protons into the lumen of the endosome  resulting drop in pH alters shape of the proteins in the endosome, allowing them to change their functions: cell surface receptors and M6P receptors release their cargo and cluster into separate vesicles (leaving behind only M6P-tagged proteins and material captured by the cell surface receptors) The Lysosome Digests Proteins, Lipids, and Nucleic Acids Lysosome  the end product of endosomal sorting  Due to activity of the proton pumps they contain, they are characteristically very acidic.  Most of the other M6P-tagged proteins that originate in RER are hydrolytic enzymes. o These are proteins that break large molecules (virus particles, proteins, lipids, nucleic acids, oligosaccharides, etc.), or sometimes even entire cells, into simpler building blocks (amino acids, fatty acids, sugars) by simply adding back water that was removed during dehydration reactions used to create them. o Glycosidic bonds, phosphoester bonds, and peptide bonds are common targets of these enzymes. o The resulting building blocks are then transported into cytosol for reuse.  are especially prevalent in many cells that are active in immune system, such as macrophages and lymphocytes, that literally engulf invaders, such as bacteria and viruses. The Peroxisome Contributes to a Number of Metabolic Activities in Cells Peroxisome  organelle that oxidizes molecules and generates hydrogen peroxide as a byproduct.  Hydrogen peroxide (HO) 2s2a potentially dangerous reactant in cells, which may explain why it is generated in its own organelle.  contains an enzyme called catalase that efficiently degrades H2 2nto water and molecular oxygen.  Many oxidation reactions taking place in peroxisomes convert long-chain fatty acids into simpler compounds that can be more easily metabolized by cells  are also capable of oxidizing toxic chemicals, thereby inactivating them.  At least some membrane proteins in peroxisomes are synthesized in the RER and delivered by vesicles, while proteins destined for interior of the peroxisome (called the peroxisomal matrix) are synthesized by free ribosomes in cytosol and pass through peroxisomal membrane after synthesis is complete. The Plasma Membrane, Endoplasmic Reticulum, Golgi Apparatus, Endosomes, Lysosomes, and Peroxisomes Form a Protein-Trafficking Network Called the Endomembrane System Endomembrane System  Is a protein-trafficking network  = Plasma Membrane + ER + Golgi apparatus + Endosomes + Lysosomes + Peroxisomes  Each different organelle performs its own specific set of cellular activities, most of the organelles found in eukaryotic cells are linked to one another via vesicles that shuttle between them.  Only organelles that do not participate in this system are nucleus, mitochondrion, and chloroplast. o Endosymbiotic theory  suggests these three organelles arose from engulfment of one cell by another, and that prokaryotes sometimes exhibit elaborate extensions of the plasma membrane.  Taken together, these observations suggest that all organelles are derived from specialized regions of plasma membrane of an ancestral prokaryotic cell. The Cytoskeleton and Motor Proteins Determine the Shape and Motion of Prokaryotic and Eukaryotic Cells Phospholipids  the hydrophobic property allows them to spontaneously assemble in an aqueous environment.  In the absence of any other force, these membranes form sphere to minimize surface-to-volume ratio.  It is important that these membranes actively participate in selective transport of molecules across them  favors an elaboration of the membrane surface.  Cells resolve this apparent paradox by employing proteins that generate force and stabilize resulting deformations in membranes. The Eukaryotic Cytoskeleton Is Composed of Three Types of Filamentous Proteins The structural components of this system (cytoskeleton) are called cytoskeletal proteins Prokaryotic cells  contain a cytoskeleton that permits them to adopt a myriad of shapes  forms the cilia and flagella they use to move through their environment. Eukaryotic cells [Members of all three classes of cytoskeletal proteins are present in each eukaryotic cell]  these relatively primitive cytoskeletal proteins evolved into larger number of proteins that are grouped into three classes (though all three form filamentous polymers). o Actin filaments  are used in many ways, including cell crawling and final division of a cell body after mitosis (called cytokinesis)  permit cells to flatten and spread to achieve a tremendous variety of shapes. o Microtubules  serve as tracks for transport of cytosolic components, including vesicles that link endomembrane system.  form mitotic spindle that ensures proper segregation of replicated chromosomes during mitosis. o Intermediate Filaments  serve as strong reinforcing material to hold cell in place once it has adopted preferred shape  proteins that generate force in this system are called motor proteins o Motor proteins bind to actin filaments or microtubules, but not intermediate filaments. o Actin-associated motor proteins generate tension necessary to deform plasma membrane, and responsible for most of motility of eukaryotic cells. o Interaction of muscle protein myosin with actin cytoskeleton, which causes contraction of skeletal muscle cells, is a good example. o Microtubule-associated motor proteins – i.e. Dynein and Kinesin  generate different kind of force, that allows them to drag membrane-bound structures in cytosol along tracks defined by microtubules.  In mitosis, these proteins are also responsible for separating two halves of mitotic spindle during anaphase. 1.5 – Cells in Multicellular Organisms Can Be Highly Specialized To Perform a Subset of the Functions Necessary for Life Multicellularity  introduced division of labor at level of cell clusters and allowed organisms to occupy environmental niches that had previously been unavailable  introduced new level of natural selection. Effective teams of cells became more INTERdependent, giving rise to larger more sophisticated organisms. Specialized Subsets of Cells Are Called Tissues Technical term of specialized teams of cells is tissue. Combination of tissues working close together = organs 4 tissue types  Epithelial, Connective, Muscle, and Nervous  Each tissue can be customized – i.e. epithelial lung tissue is different from epithelial intestinal tissue. Physiology = study of tissue and organ function Cell Differentiation Gives Rise to a Wide Variety of Cell Types Each tissue type:  Is distinct  the cells composing each tissue are quite different  the distinction arises from the types of proteins they express and how they are used. Development (Differentiation) = The process of modifying protein expression en route to the formation of a mature tissue. One of Cell Biology’s principle objectives is to understand the mechanisms that control development. Histology Is the Study of Tissues Field of Cell Biology was born when scientists developed microscopes to see cells, which are still used today. Histology = Study of tissues  cells and tissue samples are treated with special contrast agents called stains, to see structural organization better with LM and EM Epithelial Tissues Form Selectively Permeable Barriers between Distinct Body Compartments Arranged as sheets  Basal surface – cells are in contact with the basement membrane (made of fibrous material)  Apical surface – cells are in contact with the environment (varies by organ – i.e. lung – air, intestines – digested food of stomach) Many epithelial tissues are composed of multiple layers of epithelial cells each lying directly on top of layer below it. Epithelial tissue function = act as selectively permeable barrier that separates and protects the tissues on either side of the epithelial cell layer. Epithelial sheets use protein complexes (called junctional complexes) to regulate trafficking of molecules between cells and across the cell layer. Connective Tissues Provide Structural Stability to Organs For organs to be effective, cells in tissues must be organized in 3-D arrangement. CT supplies strong material necessary to maintain this arrangement much like cytoskeleton maintains the shape and organization of a single cell. Found in space between cells = extracellular matrix Extracellular matrix = complex mixture of organic and inorganic molecules that fills space between cells in CT and forms basement membrane under sheets of epithelial cells CT = consist largely of extracellular matrix molecules, populated with relatively low density of cells Examples  bone, tendon, cartilage Muscle Tissue Provides the Force Necessary to Move the Body and Pump Blood Three different types of muscle tissue  Skeletal, Cardiac, Smooth Skeletal muscle  Composed of muscle cells called myocytes  Bulk of cytosol in these cells is occupied by overlapping fibers of actin and myosin oriented in 1 direction; regions of overlap are called sarcomeres  100s of sarcomeres form  myofibrils that extend entire length of muscle cell Smooth muscle cell  Smooth muscle cells contract using actin & myosin but not organized as sarcomeres  The proteins are oriented in every direction so cells can contract in any direction necessary.  These contractions can last longer than striated muscle cells, but smooth muscle cells usually take longer to contract and don’t generate the magnitude of force that skeletal muscle does.  Smooth muscle tissue is commonly found beneath the basal surface of epithelia  Many epithelial tissues line tubes (airway in lungs, blood vessels, intestines) and the smooth muscle layer that surrounds them to control diameter of these tubes.  In the intestines, periodic contraction of smooth muscle is called peristalsis, which moves food down the GI tract. Nervous Tissue Provides for Rapid Communication between Body Parts in Animals Nervous Tissue  Transmits signals from one part of the body to another  Signals are transmitted along length of a single nerve cell like an electrical signal thru a wire  The imbalance of ions across plasma membrane (called a resting potential) is used as a tool to transmit signals.  At one end of a nerve cell (neuron), a stimulus causes proteins to permit brief exchange of ions (depolarization) across plasma membrane, and this triggers nearby proteins to do so as well.  This propagation of ion movement = action potential  travels to opposite end of the nerve cell at rapid speed and is converted into a chemical signal that diffuses to a nearby nerve cell and initiates a new action potential. Anatomists classify nerve tissues into two types:  The central nervous system, or CNS o composed of the brain and spinal cord  The peripheral nervous system, or PNS o consists of the rest of the nervous tissues in the body – i.e. nerves in the arms and legs, as well as bundles of nerves that lie outside but near the spinal cord, called ganglia. Nerves can be classified according to:  direction their action potential travels with respect to the CNS o afferent nerves carry action potentials toward the CNS, while efferent nerves (also called motor nerves) carry action potentials away from the CNS and toward effectors, which include muscles. The term nerve actually refers to a bundle of two cell types – conducting cells and support cells  Not all cells in nervous tissue conduct APs  Glial cells (support cells) actually outnumber the conducting cells. o Function is to insulate, protect, and nourish the nerve conducting cells. Plants Contain Three Classes of Tissues Plant cells are organized into three tissues:  Dermal tissue o forms the outer layers of plants, and is specialized for each plant organ (leaves, stems, and roots). o In roots, dermal tissue regulates uptake of ions and water. o consists of :  epidermal cells (usually one layer thick) that providutermost layer of protection  guard cells that form stomata on the underside of leaves to permit gas exchange.  Vascular tissue o composed of phloem and xylem  Phloem and xylem form channels that conduct water, organic solutes, and minerals  typically organized into parallel channels called vascular bundles. o provides a vascular system to move water and nutrients throughout the plant.  Ground tissue contains three different cell types that together supply new cells for growth, and provide rope-like fibers for strength. Most Diseases Are Manifested at the Level of Tissues Understanding tissue structure and function is a challenge Cancer and heart disease  two leading causes of death in the United States  not dangerous when they only


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