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Bio Lectures 11-21 notes

by: Anna Perry

Bio Lectures 11-21 notes BIOSC 0150 Zapanta - Foundations of Biology 1

Anna Perry
GPA 3.5
Foundations of Biology 1

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An outline of the book chapters in the lectures mixed with important things Zapanta said in lectures. This is useful for test 2.
Foundations of Biology 1
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This 33 page Test Prep (MCAT, SAT...) was uploaded by Anna Perry on Tuesday February 3, 2015. The Test Prep (MCAT, SAT...) belongs to BIOSC 0150 Zapanta - Foundations of Biology 1 at University of Pittsburgh taught by Zapanta in Fall2015. Since its upload, it has received 93 views. For similar materials see Foundations of Biology 1 in Biology at University of Pittsburgh.


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Date Created: 02/03/15
Lecture 11 Carbohydrates Ch 513 Sugars As Monomers Carbohydrates or sugars encompass monosaccharides 1 oligosaccharides few and polysaccharides many Carbohydrates have the molecular formula CH20nn23 Glucose and fructose share the same formula but differ structurally Monosaccharides are simple sugars and the monomers of carbohydrates The presence of a carbonyl group along with multiple hydroxyl groups provides sugars with an array of reactive and hydrophilic functional groups Three carbon sugars are trioses ve carbon sugars are pentoses ribose and six carbon sugars are hexoses glucose Carbohydrates differ in the location of their carbonyl groups and the length of their carbon skeleton Carbony group at the end of a carbon chain is an aldose Carbony group in the middle of a carbon chain is a ketose Carbohydrates can also vary in the location of their hydroxyl groups Glucose and galactose are both sixcarbon aldoses that differ only in the orientation of their hydroxyl groups Carbs can exist in linear form of a hydrocarbon chain but they tend to form ring form in aqueous solutions The ring form has two different con gurations d or B Glucose an aldohexosel Er Elmi DH 2ng DH Blame 1 aldehyde 2 2 plane E kl c EQFQUF 5 5 of ng a H r w H C DH H H I D39 al I r Hi I H 39r v 3 r v c1 c c HU c o HE D H 1 I DH H I Ell 4i y EllI Ha I 39 E DH HID Egg 1 x i I below I H c EH H Ellill plane H Elli offing EH 2DH mQI UEUEE Birglucose straightchain fcirm ring forms Fructose la ketohemsel lHl ClH H C H UH val EHEIDH ring form straightchain form II The Structure of Polysaccharides Polysaccharides or complex carbohydrates are polymers of monosaccharide monomers The simplest polysaccharides are disaccharides which are comprised of two monosaccharides Monosaccharides polymerize when a condensation reaction occurs between two hydroxyl groups resulting in a covalent interaction called a glycosidic linkage o The types of glycosidic bonds determine the structure function and stability of polysaccharides ln plant cells some monosaccharides are stored for later use in the form of starch which consists entirely of 0 glucose monomers joined by glycosidic linkages between C1 and C4 carbons Starch is a mixture of branched amylopectingtbranching occurs between C1 of on glucose and C6 of another and unbranched amylosegtd14 glycosidic linkages a glucose polymers Humans can digest starch because of d14 linkages lts 3dimensional structure forms branched and unbranched helices Glycogen performs the same storage role in animals that starch performs in plants It is a polymer of dglucose ts 3dimensional structure is highly branched helices o A cell wall is a protective sheet that occurs outside the membrane In plants and many algae cellulose is the major component of the cell wall It is a polymer of B glucose monomers joined by B14glycosidic linkages Each glucose monomer in the chain is ipped in relation to the adjacent monomer This generates a linear molecule of parallel strands joined by hydrogen bonds The linked cellulose bers are strong and give the cell structural support Humans can t digest cellulose because of the B14 linkages Chitin is a polysaccharide found in fungi cell walls some algae and many animal exoskeletons It is comprised of N acetylglucosamine NAG monomers which contain Nitrogen NAG monomers are joined by B14glycosidic linkages The geometry results in every other residue being ipped in orientation and parallel strands joined by hydrogen bonds resulting in a tough sheet that provides stiffness and protection Peptidoglycan is a structural polysaccharide found in bacteria It is the most complex of the 5 polysaccharides and has a long backbone of two alternating monosaccharides linked by B14glycosidic linkages In addition a short chain 3 to 5 of amino acids is attached to one of the two sugar types When adjacent strands align peptide bonds form between amino acids resulting in parallel strands joined by peptide bonds lll What Do Carbohydrates Do 0 In addition to serving as precursors to larger molecules carbohydrates 1 provide brous structural materials 2 indicate cell identity and 3 store chemical energy 1 Due to the strong interactions between strands consisting of B14glycosidic linkages water is excluded and the bers tend to be soluble The absence of water within these bers makes their hydrolysis more dif cult 2 The outer surfaces of cells contain glycoproteins proteins joined to carbohydrates by covalent bonds They are key molecules in cellcell recognition and cellcell signaling 3 Carbohydrates store and provide chemical energy in cells Glycogen and starch can be broken down into glucose for cells to use Phosphorylase hydrolyzes the d14glycosidic linkages in glycogen amylase hydrolyzes the d14glycosidic linkages in starch Energy stored in glucose and other carbs is used to make adenosine triphosphate ATP The chemical energy stored in the CH and CC bonds of carbohydrates is transferred to a new bond linking a third phosphate group to ADP to form ATP Plants convert the chemical energy of sunlight into the chemical energy of carbohydrates through photosynthesis Carbohydrates are so good at energy storage because they have more free energy than C02 due to the fact that CH and CC bonds have much higher potential energy than C 0 bonds This is because electrons in CH bonds and CC bonds are shared more equally and held less tightly than they are in C0 and CO bonds Lectures 12 amp 13 Lipids and Membranes Ch 613 l Lipid Structure and Function Fats store twice as much energy as carbohydrates because CH bonds have higher potential energy Lipids are carboncontaining compounds that do not dissolve readily in water They do not have a common structure and are not polymers Molecules that contain only carbon and hydrogen are known as hydrocarbons They are nonpolar because the electrons are shared equally in CH bonds Hydrocarbons are hydrophobic Fatty acids are hydrocarbon chains bonded to a carboxyl functional group All lipids have a fatty acid saturated or unsaturated Saturated hydrocarbon chains consist of only single bonds between the carbons and are solid at room temperature they pack close together because of their linear structure The longer the tall the stiffer they are Unsaturated hydrocarbon chains have one or more double bonds in the hydrocarbon chain resulting in less stored energy They are liquid at room temperature they can t pack close together because of kinks in chain Fats or triacylglycerols or triglycerides are nonpolar molecules composed of three fatty acids that are linked to a threecarbon molecule called glycerol An ester linkage joins the glycerol and fatty acid molecules via condensation reaction between a hydroxyl group of glycerol and the carboxyl group of a fatty acid Steroids are a family of lipids distinguished by a bulky fourring structure The various steroids differ from one another by the function groups or side groups attached to different carbons in those hydrophobic rings Cholesterol is a steroid that is an important component of the cell membrane in many organisms Membrane lipids are amphipathic meaning they contain both a polar hydrophilic region and a nonpolar hydrophobic region Phospholipids are the most common membrane lipids and consist of a glycerol linked to a phosphate group and two hydrocarbon fatty acid chains The head region consists of a glycerol a phosphate and a charged group It contains highly polar covalent bonds making it polar and hydrophilic The tail region is comprised of two nonpolar fatty acid chains and is hydrophobic iljiju f39ii li J r w i i m 1 u Polar a r l r 5 A l m t nah reigliri f l 1 1 I Lllliil tin IE iII l 343 mg g A wan iii FEM 7 HI EIE u n i 1 til Elli h vii l39ll quot nl 3 b F I39Ji 5 m 1139 g Equot 391 l Jl all L can WEE 7 aquot rim rm 11 0 Lipids form micelles single layer makes circle with tails on inside or lipid bilayers two layers with heads outside and tails inside in solution Phospholipid Bilayers o A lipid bilayer is created when two sheets of lipid molecules align with heads outside and tails inside They are spontaneously formed in aqueous solution due to the hydrophobic nature of the tails and the hydrophilic nature of the heads 0 When phospholipids are added to an aqueous solution lipid bilayers spontaneously form small spherical structures The hydrophilic heads on both sides of the bilayer remain in contact with the aqueous solution water is present both inside and outside the vesicle Arti cial membranebound vesicles like these are called liposomes The permeability of a structure is its tendency to allow a given substance to pass through it Phospholipid bilayers have selective permeability which means that some substances cross a membrane more easily than others Small or nonpolar molecules move across quickly Charged or large polar substances cross slowly if at all Membrane uidity refers to the movement of the lipids in a bilayer and is in uenced by 1 The number of double bonds between the carbons in the phospholipid s hydrophobic tail 2 Length of the tail 3 Number of cholesterol molecules in the membrane 4 Temperature As temperature decreases molecules in a bilayer move more slowly and the hydrophobic tails pack together more tightly How Molecules Move Across Lipid Bilayers Diffusion and Osmosis Small molecules and ions in a solution are called solutes Movement of solutes that results from their kinetic energy random motion is called diffusion A difference in solute concentration creates a concentration gradient Solutes move from regions of high concentration to regions of low concentration They will randomly distribute throughout a solution until equilibrium is established The diffusion of water across a selectively permeable membrane is called osmosis It occurs only when solutions are separated by a membrane that permits water to cross but holds back some or all of the solutes If a solution has a higher concentration of solute than the inside of a cell the outside is hypertonic relative to the inside This will cause the net ow of water out of the vesicle causing the vesicle to shrink If a solution has a lower concentration of solute than the inside of a cell the outside is hypotonic relative to the inside This will cause the net ow of water into the vesicle causing the vesicle to swell or even burst If concentrations of solute are equal the outside is isotonic relative to the inside This causes no change Lecture 14 Membrane Proteins Ch 64 Membrane Proteins Proteins that are amphipathic can be inserted into lipid biayers Ce membranes contain almost as much protein as phospholipids The FluidMosaic Model suggests that membranes are a mosaic of phospholipids and different types of proteins It is dynamic and uid Proposed by Singer and Nicolson Integral membrane proteins are embedded within the hydrophobic interior of lipid biayers They are amphipathic with a hydrophobic region that may cross the entire membrane or extend only part way into the biayer Transmembrane proteins are integral proteins that span the entire membrane and have hydrophilic segments both inside and outside the cell Can be isolated from membranes with detergents a small amphipathic molecule that interacts with the hydrophobic regions of the protein and displace the membrane phospholipids forming watersoluble detergent protein complexes Peripheral membrane proteins bind to the membrane without passing into the membrane and are found only on one side of the membrane The bind through noncovalent interactions and are often attached to integral membrane proteins Transport proteins are transmembrane proteins that transport ions and molecules that are unable to cross the membrane There are 3 broad classes of them 1 Channel proteins act as tunnels for ions or small molecules to cross a membrane They are highly selective with a certain structure allowing only a particular type of ion or molecule to pass through The movement of substances through channels does not require an input of energy Passive transport is diffusion of a substance across a membrane along an electrochemical gradient with no energy investment Facilitated diffusion is the passive transport of substances that would not otherwise cross the membrane lon channels are specialized membrane proteins that circumvent the plasma membrane s impermeability to small charged compounds lons diffuse through channels down their electrochemical gradients o CFTR is an example of a Cl39 ion channel Aquaporins are water channels that allow water to cross the cell membrane faster than it would by simple diffusion The ow of ions and small molecules through membrane channels is carefully controlled Gated channels open and close in response to a signal Carrier proteins or transporters change shape during the transport process and move molecules down a concentration gradient via passive transport GLUT1 is a glucose transporter that increases membrane permeability to glucose Pumps are membrane proteins that transport molecules across the membrane against their electrochemical gradient Movement against an electrochemical gradient requires energy in the form of ATP This process is called active transport The sodiumpotassium pump uses ATP to transport Na and K against their concentration gradient in order to make the outside of the cell more positive and the inside more negative 1 When NaKATPase begins it is in a conformation that has binding sites with a high affinity for sodium ions 2 Three sodium ions from the inside of the cell bind to these sites and activate the ATPase activity in the pump 3 A phosphate group from ATP is transferred to the pump When the phosphate group attaches the pump changes its shape in a way that opens the ionbinding pocket to the external environment and reduces its affinity for sodium ions 4 The sodium ions leave the protein and move to the exterior of the cell 5 In this conformation the pump has binding sites with a high affinity for potassium ions facing the external environment 6 Two potassium ions from outside the cell bind to the pump 7 When the potassium is bound the phosphate group is cleaved from the protein and its structure changes in response back to the original shape with the ion binding pocket facing the interior of the cell 8 In this conformation the pump has low affinity for potassium ions The potassium ions leave the protein and move to the interior of the cell 9 Cycle repeats Electrochemical gradients occur when ions build up on one side of a plasma membrane They are a combination of both a concentration gradient and a charge gradient Secondary active transport or cotransport uses an electrochemical gradient set up by a pump to power the movement of a different molecule against its concentration gradient Symporters have both molecules moving into the cell one with the concentration gradient and one against Antiporters have one substance moving into the cell and one moving in one with concentration gradient and one against Lecture 15 Water and Carbohydrate Transport in Plants Ch 38 1 amp 4 Water Potential and Water Movement Transpiration is water loss via evaporation from the aerial parts of a plant Occurs when stomata are open and the air surrounding leaves is drier than the air inside the leaves Water ows from roots to leaves without energy input passive transport due to water potential IF the potential energy that water has in a particular environment compared to the potential energy of pure water at room temperature and atmospheric pressure LJ for pure water 0 Differences in water potential determine the direction that water moves which is areas of higher LJ to areas of low LJ Two factors affect water potential 1 Solute potential tug is the potential of water to move by osmosis As solute concentration goes up solute potential goes down Solute potentials are always negative because they are measured relative to the solute potential of pure water 2 Pressure potential Ipp is the tendency of water to move in response to pressure The force exerted by the wall is called wall pressure As water moves into the cell the pressure inside the cell turgor pressure increases until wall pressure is induced 0 Cells that are rm and experience wall pressure are turgid o If there is no turgor pressure a cell is accid In the absence of pressure water moves from areas of high solute potential to low solute potential The potential energy of water in a particular location is the sum of the pressure potential and the solute potential it expedences Ws LIJP w Water potential is measured in megapascals MPa 106 Pa A water potential gradient exists between soil plants and the atmosphere Water potential is highest in soil lower in roots lower yet in leaves and lowest in the atmosphere This causes water to move up through the plant ll Translocation of Sugars Water moves along a steep waterpressure gradient from root to shoot in vascular tissue called xylem Tracheids or vessel elements The other type of vascular tissue is phloem which conducts sugars and other substances from root to shoot OR shoot to root Phloem is made of two specialized cell types sievetube elements connected to one another by perforated structures called sieve plates which create a direct connection between the cytoplasms of adjacent cells and companion cells which support the sievetube elements that don t have organelles Translocation is the movement of sugars through a plant from sources to sinks Sources are tissues where sugar enters the phloem high concentration Sinks are tissues where sugar exits the phloem low concentration The PressureFlow Hypothesis states that events at source tissues and sink tissues create a pressure potential gradient in phloem The water in phloem sap moves down this pressure gradient and sugar molecules are carried along by bulk ow Generating the pressure differences requires ATP High turgor pressure in the phloem at the source is created by movement of sugars into phloem or phloem loading which is always active transport Low turgor pressure in the phloem at the sink is created by movement of sugars out of phloem or phloem unloading which can be active or passive transport This drives phloem sap from source to sink There is a oneway ow of sucrose and a continuous loop of water movement as water is supplied to and from the xylem Proton pumps are necessary for phloem loading symporters The membrane surrounding an organelle is called the tonoplast Lecture 16 Homeostasis in Animals Ch 4313amp5 and Ch 441amp4 l Osmoregulation and Excretion Homeostasis is the stability in the chemical and physical conditions within an animal s cells tissues and organs Cells require precise concentrations of solutes to function properly Solution osmolarity is the concentration of dissolved substances in a solution 0 An electrolyte is a compound that dissociates into ions when dissolved in water They in uence osmotic balance and are required for normal membrane function Na K and Cl39 are the major ions in the human body Eectrolytes and water move through organisms by diffusion and osmosis Osmotic stress occurs when the concentration of dissolved substances in a cell or tissue is abnormal Minimizing water loss excretion of wastes and blood composition are all related to maintaining homeostasis and avoiding osmotic stress Osmoregulation is the control of water and solutes within cells Organisms such as sponges and jelly sh don t need to osmoregulate because their tissues are isotonic to seawater They are called osmoconformers Osmoregulation is required in most marine vertebrates because their tissues are hypotonic to salt water They lose water by osmosis and gain electrolytes by diffusion They gain water by drinking it and pump salt out They are called osmoregulators ll Water and Electrolyte Balance in Marine Fishes Osmoconformers maintain high urea content which increases osmolarity and makes their blood isotonic to seawater Therefore water loss is less Sharks maintain relatively low concentrations of salt in their blood by excreting NaCl through the rectal gland to counteract the diffusion into their gills from seawater Salt excretion in shark rectal gland 1 NaKATPase pumps Na out of the cell and K into the cell creating an electrochemical gradient favoring diffusion of Na into the cell and K out 2 NaCl39K cotransporter powered by the gradient favoring Na diffusion brings these three ions from the extracellular uid into epithelial cells across their basolateral surfaces 3 Cl39 diffuses into lumen along its electrochemical gradient K diffuses out through channels in basolateral membrane 4 Na diffuses into lumen along its electrochemical gradient lll Water and Electrolyte Balance in Freshwater Fishes Freshwater animals are under osmotic cells because they gain water and lose salt The elctrolyes are replaced as nutrients from food sources and by active transport from the water Fish cells are hypertonic to water IV Water and Electrolyte Balance in Terrestrial Vertebrates Land animals constantly lose water to the environment but they lose it by evaporation not osmosis ln landdwelling vertebrates osmoregulation occurs primarily through in the kidney which is responsible for water and electrolyte balance as well as the excretion of nitrogenous wastes The nephron is the basic unit of function of the kidney Water cannot be transported actively in the nephron it moves only by osmosis To move water cells in the kidney set up strong osmotic gradients By regulating these gradients and speci c channel proteins kidney cells exert precise control over loss or retention of water and electrolytes Urea is the solute that is most responsible for the steep osmotic gradient in the space surrounding the nephron The four major nephron regions and the collecting duct each have a distinct function 1 The renal corpuscle lters blood forming a ltrate or quotpreurinequot consisting of ions nutrients wastes and water 0 Filtering large volumes from the blood allows wastes to be removed effectively pairing this process with selective reabsorption allows waste excretion to occur with a minimum of water and nutrient loss 2 Filtrate leaves Bowman39s capsule and enters a convoluted structure called the proximal tubule where epithelial cells reabsorb nutrients vitamins valuable ions and water 0 NaKATPase in the basolateral membranes removes Na from the interior of the cell The active transport of sodium ions out of the cell creats a gradient favoring the entry of Na from the lumen o In the apical membrane adjacent to the lumen Na dependent cotransporters use this gradient to remove valuable ions and nutrients selectively from the ltrate The movement of Na into the cell along its concentration gradient provides the means for moving other solutes against their concentration gradient 0 The solutes that move into the cell diffuse across the basolateral membrane into the interstitial uid via channel proteins and the nearby blood vessels 0 Water follows the movement of ions from the proximal tubule into the cell and then out of the cell and into blood vessels via aquaporins 3 The loop of Henle establishes a strong osmotic gradient in the tissues outside the loop and osmolarity increases as the loop descends 0 As uid ows down the descending limb the uid inside the loop loses water to the interstitial uid surrounding the nephron This is passive transport 0 At the bottom of the loop the inner medulla the uids inside and outside the nephron have high osmolarity The ltrate does not continue to lose water through because the membrane in the ascending limb is nearly impermeable to water 0 The uid inside the nephron loses Na and CI39 in the thin ascending limb passively 0 Additional Naand Cl39 ions are actively transported out of the nephron in the thick ascending limb o The countercurrent ow of uid combined with changes in permeability to water and in the types of channels and pumps that are active in the epithelium of the nephron creates a self reinforcing system 0 The presence of an osmotic gradient stimulates water and ion ows that in turn maintain an osmotic gradient 4 Once the ltrate has passed through the Loop of Henle the major solutes it contains are urea other wastes and a low concentration of ions Na and Cl39 In the distal tubule ions and water are reabsorbed The ltrate entering is always dilute 5 The collecting duct may reabsorb more water to maintain homeostasis Urea leaves the base of the collecting duct and contributes to the osmotic gradient set up by the loop of Henle Hormones signaling molecules regulate water and electrolyte balance in the distal tubule and collecting duct lf Na levels in the vlood are low the adrenal glands release the hormone aldosterone which leads to activation of sodiumpotassium pumps and reabsorption of Na in the distal tubule Water follows by osmosis Aldosterone saves sodium and water If an individual is dehydrated the brain releases antidiuretic hormone ADH ADH saves water 1 ADH triggers the insertion of aquaporins into the apical membrane As a result cells become much more permeable to water and large amounts of water are reabsorbed 2 ADH increases permeability to urea which is reabsorbed into the surrounding uid The helps create a concentration gradient favoring water reabsorption from the ltrate Nutritional Requirements A carbohydrate protein or fat is an example of a nutrient Too much of a nutrient or too little can be problematic or even fatal Diabetes mellitus disrupts glucose homeostasis People with this disorder experience abnormally high levels of glucose in their blood Insulin is a hormone that is secreted by the pancreas when blood glucose levels are high It travels through the blood stream stimulating cells in the liver and skeletal muscle to import glucose from the blood and synthesize glycogen from glucose monomers As a result blood glucose levels decline negative feedback The pancreas secretes Glucogen when blood glucose levels fall lt stimulates the liver to break down glycogen and make glucose As a result blood glucose levels increase negative feedback In response to glucagon cells in the liver catabolize glycogen and also produce glucose via gluconeogenesis the synthesis of glucose from noncarbohydrate compounds People with type 1 diabetes are insulin dependent and do not produce insulin because cells that produce insulin in the pancreas are destroyed People with type 2 diabetes are noninsulin dependent and make insulin but are resistant to it because it does not bind properly to receptors on target cells More likely to be obese Lecture 17 Prokarvotic Cells Ch 71 and 291amp3 Bacterial and Archaeal Cell Structures and Their Functions Cells are divided into eukaryotes and prokaryotes This is based on cell morphology or shape Eukaryotic cells have a membranebound nucleus and prokaryotic cells do not All cells have nucleic acids proteins carbohydrates and a plasma membrane A prokaryote is an organism without a membranebound nucleus There are two domains bacteria and archaea A prokaryotes have a plasma membrane a single chromosome ribosomes and a stiff cell wall Most prokaryotic species have a supercoiled circular chromosome in the nucleoid region of the cell Many bacteria contain small circular DNA molecules called plasmids They are physically independent of the cellular chromosome Ribosomes are found in the cell interior and are complex structures composed of large and small subunits that contain RNA and protein molecules Most prokaryotes have a stiff cell wall necessary because the cell is hypertonic to the environment and needs it so it won t burst There are two general types of cell wall that can be distinguished by treatment with a dye called the Gram stain 1 Grampositive cells have a cell wall containing an extensive amount of peptidoglycan holding the stain better purple 2 Gramnegative cells have a cell wall with a thin peptidoglycan layer surrounded by an outer phospholipid biayer pink Some prokaryotes have taillike agella which help in movement or needlelike projections called mbriae which promote attachment to other cells or surfaces Many prokaryotes have internal photosynthetic membranes Why Do Biologists Study Bacteria and Archaea Bacteria have a unique compound called peptidoglycan in their cell walls Archaea have unique phospholipids in their plasma membranes the hydrocarbon tails of the phospholipids are made from isoprene They are unicellular Most microbes microscopic organisms are bacteria and archaea Recently organelles have been discovered in many bacterial species that store ions hold magnetite crystals organize enzymes or sequester enzymes Bacteria and archaea show extensive morphological diversity in terms of size shape and motility Bacteria or archaea that live in highsalt hightemperature lowtemperature or highpressure habitats are extremophiles Of the thousands of bacterial species living in and on your body only a tiny fraction can disrupt normal body functions enough to cause illness Bacteria that cause disease are said to be pathogenic Robert Koch hypothesized that bacteria might be responsible for causing infectious diseases Koch s experimental results were the rst test of the germ theory of disease Koch39s postulates 1 The microbe must be present in individuals suffering from the disease and absent from healthy individuals 2 The organism must be isolated and grown in a pure culture away from the host organism 3 If organisms from the pure culture are injected into a healthy experimental animal the disease symptoms should appean 4 The organism should be isolated from the diseased experimental animal again grown in pure culture and demonstrated by its size shape and color to be the same as the original organism Antibiotics are molecules that kill bacteria or stop them from growing Bioremediation is the use of bacteria and archaea to clean up sites polluted with organic solvents lll What Themes Occur in the Diversi cation of Bacteria and Archaea Bacteria and Archaea produce ATP in 3 ways 1 Phototrophs use light energy to excite electrons ATP is produced by photophosphorylation Cyanobacteria were the rst organisms to produce oxygen through photosynthesis Organisms that use water as a source of electrons for photosynthesis complete oxygenic photosynthesis Many phototrophic bacteria use a molecule other than water as the source of electrons This is anoxygenic photosynthesis 2 Chemoorganotrophs oxidize organic molecules with high potential energy such as sugars ATP may be produced by cellular respiration with sugars serving as electron donors or via fermentation pathways 3 Chemolithotrophs oxidize inorganic molecules with high potential energy such as ammonia NH3 or methane CH4 ATP is produced by cellular respiration and inorganic compounds serve as the electron donor Bacteria and archaea ful ll their second nutritional need obtaining buildingblock compounds with carboncarbon bonds in two ways 1 By synthesizing their own compounds from simple starting materials such as C02 and CH4 organisms that manufacture their own buildingblock compounds are called autotrophs 2 By absorbing readytouse organic compounds from their environment organisms that acquire building block compounds from other organisms are called heterotrophs Certain bacteria and archaea are the only species that are capable of converting molecular nitrogen to ammonia through nitrogen xation Lecture 18 Eukaryotic Cells Animal Cells amp Plant Cells Ch 726 l Eukaryotic Cell Structures and Their Functions 0 Because eukaryotic cells are subdivided the cytoplasm the uid portion between the plasma membrane and these organelles is only a fraction of the total cell volume Unlike prokaryotes eukaryotes have a membrane bound nucleus where chromosomes are found A complex double membrane called the nuclear envelope which is studded with porelike openings where traf c across the nuclear envelope occurs encloses the nucleus The inside surface is linked to brous proteins that form a latticelike sheet called the nuclear lamina which stiffens the structure and maintains its shape Chromosomes do not oat freely inside the nucleus Each occupies a distinct area The nucleus also contains speci c sites where gene products are processed and includes at least one distinctive region called the nucleolus where RNA molecules are manufactured Nuclear proteins are synthesized by ribosomes in the cytosol and contain a common amino acid sequence that marks them for transport into the nucleus The portions of the nuclear envelope extend into the cytoplasm to form the endoplasmic reticulum The Rough ER is dotted with ribosomes It is involved in synthesis of plasma membrane proteins secreted proteins and proteins localized to the ER Golgi apparatus and lysosomes o The interior of the rough Eris called the lumen It is where newly manufactured proteins undergo folding and other types of processing The smooth ER contains enzymes that catalyze reactions involving lipids It also functions as a reservoir for calcium ions Proteins are transported from the ER to the Golgi apparatus in vesicles The products of the rough ER pass through the Golgi apparatus which consists of discrete attened membranous sacs called cisternae which are stacked on top of one another The Golgi apparatus receives products cis and ships them trans out to other organelles or the cell surface Animal cells contain lysosomes which function as recycling centers and contain enzymes specialized for hydrolyzing different types of macromolecules The endomembrane system is formed by lysosomes the golgi apparatus and the ER Instead of lysosomes plant and fungi cells contain vacuoles which are specialized for digestion or storage All eukaryotic cells contain globular organelles called peroxisomes which are centers for reductionoxidation reactions Glyoxysomes are specialized peroxisomes that are packed with enzymes that oxidize fats to form a compound that can be used to store energy for the cell Cell Systems Nuclear Transport The nuclear envelope is broken with openings called nuclear pores which connect the inside of the nucleus with the cytosol Each pore consists of over 50 different proteins which form an elaborate structure called the nuclear pore complex Nuclear proteins are synthesized by ribosomes in the cytosol and contain a quotzip codequot that marks them for transport through the nuclear pore complex This is nuclear localization Cell Systems II The Endomembrane System Manufactures Ships and Recycles Cargo The secretory pathway hypothesis proposes that proteins intended for secretion from the cell are synthesized and process in a highly prescribed set of steps The PulesChase experiment supports this hypothesis The pulse expose experimental cells to a high concentration of a modi ed amino acid for a short time The chase The pulse ends by washing away the modi ed amino acid and replacing it with the normal version of the same molecule A sequence of amino acids that will move proteins in the ER lumen is called the ER signal sequence As the protein is being synthesized on the ribosome a signal recognition particle in the cytoplasm binds to the ER signal sequence The SRP binds to a SRP receptor in the ER membrane 1 Protein synthesis begins on a free ribosome in the cytosol The ribosome synthesizes the ER signal sequence 2 The signal sequence binds to a signal recognition particle The attached SRP causes protein synthesis to stop 3 The ribosome signal sequence SRP complex moves to the ER membrane where it attaches to the SRP receptor 4 Ones the receptor and SRP connect the SRP is released and protein synthesis continues 5 The growing protein is fed into the ER lumen through a channel and the signal sequence is removed Because carbs are polymers of sugar monomers the addition of one or more carb groups is called glycosylation Each protein coming out of the Golgi apparatus has a molecular tag that places it in a particular type of transport vesicle Some are sent to the cell surface where they fuse with the plasma membrane and release the contents to the exterior of the cell This is exocytosis Endocytosis refers to the pinching off of the plasma membrane resulting in the uptake of material from outside the cell Receptormediated endocytosis 1 Macromolecules outside the cell bind to membrane proteins that act as receptors 2 The plasma membrane folds in and pinches off to form an endocytic vesicle 3 The endocytic vesicle fuses with an early endosome activating protons that lower its pH Cargo is released and empty receptors are recycled to the surface 4 The early endosome matures into a late endosome that receives digestive enzymes from the Golgi apparatus 5 The late endosome matures into a functional lysosome and digests the endocytosed macromolecules Autophagy is the process by which damaged organelles are surrounded by a membrane and delivered to a lysosome to be recycled ln phagocytosis the cell plasma membrane surrounds another cell or food particle and engulfs it Cell Systems Ill The Dynamic Cytoskeleton The cytoskeleton is a dense and complex network of bers that helps maintain cell shape by providing structural support lts brous proteins move and change to alter the cell s shape shift its contents or move the cell itself There are three types of cytoskeletal proteins 1 Actin laments micro laments are brous structures made of actin Smallest cytoskeletal elements Formed by polymerization of individual actin molecules Grouped together into long bundles or dense networks inside the plasma membrane lnteracts with the motor protein myosin to cause cellular movement A motor protein is a protein that converts the potential energy in ATP into the kinetic energy of mechanical work actin is a motor protein like myosin ATPpowered interaction between actin and myosin is the basis for cytokinesis cell division cytoplasmic streaming the directed ow of cytosol and organelles within plant cells and cell crawling which occurs when groups of actin laments grow creating bulges in the plasma membrane that extend and move the cell 2 Intermediate laments provide structural support to the cell Made of keratins lamins or others Nuclear lamins which make up the nuclear lamina qualify as intermediate laments ntermediate laments form a exible skeleton that helps shape the cell surface and hold the nucleus in place 3 Microtubules are large hollow tubes made of two polypeptides dtubulin and Btubulin that exist as stable protein dimers Microtubules originate from the microtubule organizing center Their plus ends grow outward radiating throughout the cell In animals the microtubule organizing center is the centrosome which contains two bundles of microtubules called centrioles Microtubules are also involved in movement and act as quotrailroad tracksquot Transport vesicles move through the cell along these tracks in an energydependent process Kinesin hydrolyzes ATP to walk along a microtubule track Bacterial agella are helical rods consisting of several microtubules and move the cell by rotating the rod like a propeller Cilia are short hairlike projections Flagella and cilia consist of several microtubules that form an axoneme Movement occurs when the motor protein dynein uses ATP and walks up the microtubules Lecture 19 Eukaryotic Cells What is a Protist Ch 3013 Why Do Biologists Study Protists Eukaryotes are larger cells with more organelles and have a cytoskeleton They also have a nuclear envelope Multicellularity is common and they reproduce sexually and asexuaHy Protists are a group of organisms that include all eukaryotes except the land plants fungi and animals Protists are a paraphyletic group they represent some but not all of the descendants of a single common ancestor There is no single trait that they all share Malaria is a highly infectious disease caused by the protist Plasmodium Pasm0dium cells enter a person s bloodstream during a mosquito bite and it initially infects liver cells The Plasmodium cells change into a distinctive cell type that infects red blood cells They then multiply asexually and continue to infect red blood cells which burst n mosquito host sexual reproduction takes place in the gut and salivary glands In human host asexual reproduction takes place and infects and kills liver cells and red blood cells contributing to anemia and high fever Algal blooms are when a unicellular species experiences rapid population growth and reaches high densities in an aquatic environment Can be harmful to people because clams and other shell sh lter photosynthetic protists out of the water as food During a bloom high levels of toxins can build up in the esh of these shell sh Dino agellates are a group of protists that live in freshwater They are photosynthetic and make up the largest group of protists Have tough plates in cell wall made of cellulose Have chromosomes that lack histones and attach to nuclear envelope Protists play a key role in aquatic food chains the nutritional relationships among organisms and how energy ows through ecosystems Many of the species at the base of food chains in aquatic environments are protists Photosynthetic protists take in carbon dioxide from the atmosphere and reduce or x it to form sugars or other organic compounds with high potential energy In this way they are primary producers Diatoms are photosynthetic protists that rank among the leading primary producers in the oceans simply because they are abundant Diatoms and other small organisms that drift in the open oceans or lakes are plankton o Photosynthetic plankton are phytoplankton which form the base of food chains The carbon atoms in carbon dioxide molecules move to organisms on land or in the oceans and then back to the atmosphere in what is called the global carbon cycle Protists play a key role in the global carbon cycle and act as carbon sinks that could help reduce global climate change ll How Do Biologists Study Protists Detailed studies reveal that protists can be grouped according to overall cell structure according to organelles with distinctive features The agellum is an organelle that projects from the cell and whips back and forth to produce swimming movements There are seven major groups of eukaryotes Fungi and animals form a monophyletic group called Unikonta The other ve major lineages form a monophyletic group called the Bikonta lll What Themes Occur in the Diversi cation of Protists The common feature among protists is that they tend to live in environments where they are surrounded by water The earliest eukaryotes were probably single celled organisms with Mitochondria A nucleus An endomembrane system ER and golgi No cell wall A type of agellum The endosymbiosis theory proposes that mitochondria originated when a bacterial cell took up residence inside another cell Mitochondria are about the size of an average bacterium Mitochondria replicate by ssion like bacteria They have their own ribosomes and manufacture their own proteins They have double membranes They have their own genomes organized as circular molecules like bacterial chromosomes The leading hypothesis for the origination of the nuclear envelope is that it is derived from the infoldings of the plasma membrane lnfodings would have given rise to the endoplasmic reticulum at the same time Protists feed in various ways 1 lngestive feeding is based on eating live or dead organisms by engul ng them Phagocytosis is when a cell takes in packets of food much larger than individual molecules 0 This can be done in protists that lack a cell wall 0 Can be done by using long ngerlike projections called pseudopodia Other ingestive feeders attach themselves to a surface and feed by sweeping food into their mouth with cilia 2 Absorptive feeding occurs when nutrients are taken directly from the environment across the plasma membrane usually through transport proteins Some absorptive feeders are decomposers feeding on dead organic matter or detritus Many absorptive feeders live inside other organisms If it damages its host it is called a parasite 3 Photosynthesis is carried out by autotrophic protists The endosymbiosis theory contends that the eukaryotic chloroplast originated when a protist engulfed a cyanobacterium The bacterium provided its host with oxygen and glucose in exchange for protection and access to light Primary endosymbiosis Chloroplasts have bacterialike characteristics Many animal and protist cells have endosymbiotic cyanobacteria Choropasts have a circular DNA molecule containing genes that are similar to cyanobacterial genes One group of protists has a chloroplast with an outer layer of peptidoglycan which is found in the cell walls of cyanobacteria Secondary endosymbiosis occurs when an organism engulfs a photosynthetic eukaryotic cell and retains its chloroplasts as intracellular symbionts The chloroplasts found in some protists have four membranes which could be the result of this Protists use their pseudopodia for amoeboid motion a sliding movement that requires ATP Other major modes of locomotion involve swimming via agella or cilia Sexual reproduction which is based on meiosis and fusion of gametes results in daughter cells that are genetically different from their parents and from each other originated in protists Asexual reproduction is based on mitosis and cell division in eukaryotic organisms and results in daughter cells that are genetically identical to the parent A life cycle describes the sequence of events that occur as individuals grow mature and develop Some protists have life cycles dominated by haploid cells one copy of each chromosome ie Gametes Others have life cycles dominated by diploid cells two copies of each chromosome ie Human cells Some protists have life cycles that alternate between haploid and diploid forms known as alternation of generations Lecture 20 amp 21 Energy and Enzymes Ch 814 What Happens to Energy in Chemical Equations Chemical reactions require energy the capacity to do work or supply heat Free energy is the amount of energy that is available to do work Energy exists in two forms 1 Kinetic energy is the energy of motion In molecular systems this is molecular motion or thermal energy temperature 2 Potential energy is stored energy associated with position or con guration In molecular systems this is stored in chemical bonds chemical energy The First Law of Thermodynamics stats that energy cannot be created or destroyed only transferred and transformed The total energy in a molecule is referred to as its enthalpy H This includes the potential energy of the molecule plus the effect of the molecule on its surroundings in terms of pressure and volume When a reaction releases heat energy it is exothermic 0 Products lt Reactants in potential energy 0 AH is negative f heat energy is taken up during the reaction it is endothermic 0 Products gt Reactants in potential energy 0 AH is positive The Second Law of Thermodynamics states that systems tend to proceed from a state of order to a state of disorder randomness Entropy S is a measure of the amount of disorder in a system 0 When products of a chemical reaction become less ordered than the reactant molecules entropy increases AS gt0 0 The entropy of the universe is always increasing The Gibbs free energy change AG of a reaction is the amount of energy available to do work usable energy It takes into account the change in total energy AH and the change in entropy AS It also is equal to the difference in free energy between the products and the reactants AG AH TAS 39AGreaction Gproducts Greactants AG determines whether a reaction requires added energy to proceed If the free energy of the products is lower than the free energy of the reactants the reaction is exergonic AG lt O Spontaneous reaction No energy required Products lt Reactants If the free energy of the products is higher than the free energy of the reactants the reaction is endergonic AG gt 0 Not spontaneous Energy required Products lt Reactants AG 0 means equilibrium Nonspontaneous Reactions May Be Driven Using Chemical ReacUons Energetic coupling between exergonic and endergonic reactions allows the chemical energy released from one reaction to drive another reaction Exergonic gives off energy that endergonic need to react making the sum of reactions exergonic Energy doesn t come from ATP it comes from the hydrolysis of ATP which is another reaction The hydrolysis of ATP is exergonic Negative phosphate charges are unfavorable but are held together despite repulsions If one phosphate goes away there s less negativity and the electrical charge is spread out making ADP more stable Coupling nonspontaneous reactions with ATP hydrolysis enables the reactions to proceed making them exergonic Reductionoxidation reactions redox reactions are chemical reactions that involve electron transfer When an atom gains an electron it is reduced Reduction is the gain of one or more electrons Reduction often adds an When an atom or molecule loses an electron it is oxidized Oxidation is the loss of one or more electrons Oxidation often removes an Oxidation and reduction events are always coupled Electron donors are always paired with electron acceptors Flavin adenine dinucleotide FAD is a cellular electron acceptor that is reduced by two electrons accompanied by two proteins to form FADH2 which readily donates these electrons to other molecules It has quotreducing powerquot Nicotinamide adenine dinucleotide NAD is another common electron carrier and is reduced to form NADH A kilocalorie of energy raises 1 kilogram of water 1 C How Enzymes Work The rate of a spontaneous reaction can be increased by increasing temperature or the concentration of reactants Enzymes catalyze reactions by bringing reactants together in precise orientations or by stabilizing the transition states of chemical reactions A substrate is a reactant that interacts with a catalyst in a reaction The addition of a phosphate group to a substrate is called phosphorylation This changes activity because a phosphate group is negatively charged and therefore changes the charge of the enzyme changing its structure and therefore function Substrates bind to an enzyme s active site Most enzymes undergo a conformational change when the substrates are bound to the active site This is induced t which reorients the substrates and binds them tighter to the active site The activation energy Ea of a reaction is the amount of free energy required to reach the intermediate condition or transition state lnteractions between the enzyme and the substrate stabilize the transition state and lower the activation energy required for the reaction to proceed AG does not change Cannot make a nonspontaneous reaction spontaneous Enzymes are not changes or used up in the reaction Atoms or molecules that are not part of an enzyme s primary structure are often required for an enzyme to function normally 1 Cofactors Inorganic ions which reversibly interact with enzymes meaning they are not permanently associated with them 2 Coenzymes Organic molecules that reversibly interact with enzymes such as NADH or FADH2 3 Prosthetic groups Nonamino acid atoms or molecules that are permanently attached to proteins such as heme or retinal IV What Factors Affect Enzyme Function Enzymes have an optimal temperature and pH and will denature if not in an ideal situation Enzymes are often regulated activated or inactivated in response to cellular conditions 1 Competitive inhibition occurs when a molecule similar in size and shape to the substrate competes with the substrate for access to the active site nhibits catalysis by binding to the active site Can be overcome by adding more substrate 2 Allosteric regulation occurs when a molecule causes a change in enzyme shape by binding to the enzyme at a location other than the active site Makes active site available or unavailable Prevents substrate from binding slows rate or helps it bind better increases rate Covalent modi cation is a chemical change to the enzymes primary structure that alters the function of the enzyme Phosphorylation is the most common modi cation which changes the shape and activity of proteins These modi cations are reversible ie Dephosphorylation


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