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Biology 150 Fall 39 Life amp Its Chemistry continued PART 2 Answers THE CHEMICAL BUILDING BLOCKS OF LIFE THE GRAND SCHEME 1 PROTEINS De ne what a protein is andor of what it is made Being in favor of young people is not a valid answer Protein A protein is a 3D polymer constructed from a set of 20 different monomeric units called amino acids Proteins consist of one or more polypeptide chains folded into a unique three dimensional shape or conformation Each polypeptide chain consists of a particular unique sequence of amino acids This sequence is referred to as the protein39s primary structure and it determines the chemical properties and further structures of the protein The pleated folding or helical coiling of the chain is called the secondary structure of the protein The tertiary structure refers to the complex three dimensional globular structure assumed by some proteins as their polypeptide chains bend and ball up Finally a protein is said to have a quaternary structure if it has more than one polypeptide chain quaternary structure refers to how these chains are shaped and associated with each other The structure of a protein is responsible for the way it mctions De ne all the different lnctions that a protein may have Enzymes catalytic activity carry out biological chemical reactions and functions A gt B Transport Proteins bind amp carry molecules from one point to another Storage Proteins store amino acids C H O amp N for later use Ex ovalbumin egg white ferretin iron protein of bacteria casein a milk protein Contractile can contract change shape responsible for movement actin and myosin in muscle make up the elements of cytoskeleton amp muscles Structural Support collagen of tendons elastin of ligaments keratin of hair amp feathers broin of silk amp spider webs Defensive protect make up antibodies IgG etc brinogen amp thrombin coagulation protein of blood snake venom39s phosphodiesterases enzymes digest nucleic acids Regulatory regulate many metabolic processes ie hormones and internal physiological control transcription factors amp enhancers which help DNA genes make other proteins NUCLEIC ACIDS De ne what a nucleic acid is andor of what it is made How many different kinds of nucleic acids can you name Which Came First DNA or RNA and why Nucleic acids store and transmit hereditary information Genes are the units of inheritance which determine the primary structure of proteins Nucleic acids are macromolecules that carry and translate this code DNA deoxyribonucleic acid is the genetic material that is inherited from one generation to the next and is reproduced cell division mitosis and meiosis in each cell of an organism RNA ribonucleic acid reads the instructions coded in DNA and directs the synthesis of proteins the ultimate enactors of the genetic program In a eukaryotic cell DNA resides in the nucleus and messenger RNA carries the instructions for protein synthesis to ribosomes located in the cytoplasm DNA molecules consist of two chains of nucleotides spiraling around an imaginary axis in a double helix In 1953 Watson and Crick rst proposed this double helix arrangement which consists of two sugarphosphate backbones on the outside of the helix with their nitrogenous bases pairing and hydrogenbonding together on the inside Adenine always pairs with only thymine guanine always pairs with cytosine Thus the sequences of nitrogenous bases on the two strands of DNA are complementary to each other Because of this speci c base pairing property DNA can replicate itself and precisely copy the genes of inheritance There are at least 6 different types of nucleic acids 1 DNA the genetic material of most cells 2 ribosomal RNA rRNA which makes up the ribosome the site of protein synthesis in cells 3 transfer RNA tRNA which carries an amino acid to the ribosome for protein synthesis 4 messenger RNA mRNA is a complementary copy of the DNA genes which codes for the amino acid sequence in a newly made protein 5 heterogeneous nuclear RNA hnRNA which is the primary copy of the DNA into an RNA product and is the precursor of mRNA 6 small nuclear ribonuclear particles snRNP which is a particle like a ribosome that speci cally cuts hnRNA into smaller pieces of mRNA BIL 150 Chemistry an Part 2 answers pg 1 Most nucleic acid biochemists today believe that RNA came before DNA The main evidence to support this premise is l the ability of some RNA s of today to replicate themselves 2 the fact that some small RNA pieces called introns have catalytic activity and can cut other RNA molecules and 3 the idea of complimentary templating where a randomly assembled RNA can makes its own compliment which can then make back the original RNA sequence Remember most of these observations are speculative and border on the realm of ironic sciencevin that they are not fully experimentally testable i hypotheses 2 Some KEY TERMS in the Chemistry of Life De ne each of the terms given below macromolecule a very large molecule usually composed of a polymer of monomeric units linked together via condensation reactions into a long chain molecule Examples include polysaccharides proteins and nucleic acids polymer 39 a chemical compound or mixture of compounds formed by polymerization and consisting essentially of repeating individual structural units monomers enzyme word derived from the Greek quoten zymequot leaven 1881 any of numerous complex proteins that are produced by living cells and catalyze speci c biochemical reactions at body temperatures 39 active site The active site is an enzyme s catalytic center a closer look The substrate is held in the active site by hydrogen or ionic bonds creating an enzymesubstrate complex The side chains R groups of some of the surrounding amino acids in the active site facilitate the conversion of substrate to product The product then leaves the active site and the enzyme can bind with another substrate molecule Enzymes can catalyze reactions involving the joining of two reactants by providing active sites in which the substrates are bound closely together and properly oriented An induced t can stretch or bend critical bonds in the substrate molecule and make them easier to break An active site provides a microenvironment such as a lower pH that is necessary for a particular reaction Enzymes may also actually participate in a reaction by forming brief covalent bonds with the substrate The rate at which an enzyme molecule works partly depends on the concentration of its substrate The speed of a reaction will increase with increasing substrate concentration up to the point at which all enzyme molecules are saturated with substrate molecules and working at full speed Peptide A term commonly used by biochemists and biologists to describe very short proteins any of various polymers that are made from two or more amino acids linked by a combination of the amino group of one acid with the carboxyl group of another a byproduct obtained by partial hydrolysis of whole proteins Polypeptide A linear chain of many amino acids more than a peptide but less than a protein a term often used as analogous to the word 39protein39 cofac tor Cofactors are small molecules that bind with enzymes and are necessary for enzyme catalytic function They may be inorganic such as Various metal atoms Fe Mn Co Zn Mg or large organic molecules called coenzymes Most vitamins are coenzymes or precursors of coenzymes amino acid Most amino acids are composed of an asymmetric carbon bonded to a hydrogen a carbonyl group an amino group and a variable side chain called the R group The R group confers the unique physical and chemical properties of each amino acid Side chains may be either nonvpolar and hydrophobic or polar or charged and thus hydrophilic Acidic side chains contain carboxyl groups and are usually negatively charged basic side chains contain an amino group and are usually positively charged peptide bond A peptide bond links the amino group of one amino acid with the carboxyl group of another yielding a polymer of amino acids called a polypeptide The polypeptide chain has a free carboxyl group at one end and a free amino group at the other end Polypeptides vary in length from a few amino acids to a thousand or more amino acids conformation A protein39s function depends on its speci c conformation which is any of the spatial arrangements of a molecule that can be obtained by rotation of the atoms about a single bond Proteins have unique threedimensional shapes created by the twisting or folding of one or more polypeptide chains The unique conformation of a protein which results from its sequence of amino acids enables it to recognize and bind to other molecules BIL 150 Chemistry m Part 2 answers pg 2 4 primary structure secondary structure tertiary structure quaternary structure Four Levels of Protein Structure There are three structural levels in the conformation of a protein A fourth level may be present when a protein consists of more than one polypeptide chain Primary structure is the unique genetically coded sequence of amino acids within a protein ie a slight deviation from the sequence of amino acids can severely affect a protein39s function by altering the protein39s conformation In the early 19503 Fred Sanger determined the primary structure of insulin through the laborious process of hydrolyzing the protein into small peptide chains using chromatography to separate the small pieces determining their amino acid sequences and then overlapping the sequences of small fragments created with different agents to reconstruct the whole polypeptide Most of these steps are now automated and can be done in an afternoon Secondary structure involves the coiling or folding of the polypeptide backbone stabilized by hydrogen bonds between the electronegative oxygen of one peptide bond and the weakly positive hydrogen attached to a nitrogen of another bond An alpha helix is a delicate coil produced by hydrogen bonding between every fourth peptide bond A pleated sheet is also held by repeated hydrogen bonds along the protein39s backbone This secondary structure forms when the polypeptide chain folds back and forth or when regions of the chain lie parallel to each other Interactions between the various side chains of the constituent amino acids produce a protein39s tertiary structure Hydrophobic interactions between nonpolar side groups in the center of the molecule hydrogen bonds and ionic bonds between negatively and positively charged side chains produce the stable and unique shape of the protein Strong covalent bonds called disulfide bridges may occur between the sul iydryl side groups of cysteine monomers that have been brought close together by the folding of the polypeptide Quaternary structure occurs in proteins that are composed of more than one polypeptide chain The individual polypeptide subunits are held together in a precise structural arrangement disul de bridges a covalent linkage between two sulfhydryl SH groups on the amino acids cysteine Commonly joins or links two proteins or two different parts of the same protein together S S enzyme inhibitors Enzyme Inhibitors Enzyme inhibitors selectively disrupt the action of enzymes either by reversibly binding with the enzyme via weak electrostatic bonds or by irreversibly attaching often via covalent bonds Competitive inhibitors compete with the substrate for the active site of the enzyme Increasing the concentration of substrate molecules may overcome this type of inhibition Noncompetitive inhibitors bind to a part of the enzyme separate from the active site and change the conformational shape of the enzyme thus impeding enzyme action Many pesticides and antibiotics are inhibitors of key enzymes and act as metabolic poisons chaperone proteins heat shock proteins Chaperone proteins help the intracellular folding of proteins The amino acid sequences of hundreds of proteins have been determined Using the technique of Xray crystallography coupled with computer modeling and graphics biochemists have established the 3D shape of many of protein molecules Researchers have developed methods for following a protein through its intermediate conformational states on the way to its nal form and have discovered chaperone proteins which assist the folding of other proteins Originally called heat shock protein these molecules protect other proteins by changing their shapes and conformations As protein folding becomes better understood scientists are learning to produce amino acid sequences for proteins that will be able to perform predetermined functions globular proteins any protein with an approximately rounded 3D shape Most enzymesjare globular shaped allosteric regulation Allosteric Regulation inhibition regulation of enzyme activity by the binding of a regulator molecule to an allosteric site a receptor site separate from the active site Complex enzymes made of two or more polypeptide chains each with its own active site may have allosteric sites located where subunits join The entire unit may oscillate between two conformational states and the binding of an activator or inhibitor stabilizes the catalytically active or inactive conformation Allosteric enzymes are often critical regulators of metabolic pathways brous proteins a protein with an elongated shape typically one such as collagen or an intermediate lament protein which are able to associate into long filamentous structures BIL 150 Chemistry m Part 2 answers pg 3 nucleotides Nucleotides are the building block units of nucleic acids Each nucleotide consists of a vecarbon sugar ribose or deoxy ribose a phosphate group and a nitrogenous base AUGC and T Nucleotides are also components of other biologically important compounds such as ATP and the coenzyme NAD phosphodiester bond Nucleotides are linked together into a DNA polymer by phosphodjester covalent bonds which join the phosphate of one nucleotide with the sugar of the next The nitrogenous bases extend from this repeating sugarphosphate backbone The unique sequence of bases in a gene codes for the speci c amino acid sequence of a protein purines one of the two categories pyrimidines being the other of nitrogencontaining heterocyclic ring 2 rings compounds found in DNA and RNA Examples include adenine and guanine Pyrimidines one of the two categories purines being the other of nitrogencontaining cyclic ring 1 ring compounds found in DNA and RNA Examples include cytosine thymine and uracil adenine A guanine G cytosine C thymine T uracil U double helix the typical conformation of a DNA molecule in which two strands are would around each other with hydrogen bonding base pairing between the two strands 3 Match the following numbers with an appropriate statement A number may be used more than once Numbers 0 1 2 3 4 5 6 12 20 Statements a the number 5 of different nitrogenous bases in DNA b the number 3 of different chemical classes of amino acids c the number 2 of chains of nucleotides in a DNA molecule 1 the number 4 of different nitrogenous bases in RNA e the number 20 of different amino acids found in proteins f the number 1 of chains of nucleotides in most RNA molecules LEARNING CHECKLIST 1 What is the building block unit of proteins How do these building blocks differ from each other The building blocks are amino acids which are organic molecules that contain both an amino groups at one end and an acid group carboxyl at the other end Alpha amino acids are those in which the amino group and the carboxyl group are linked to the same carbon atom The amino acids differ from each other in the composition of a 39side group39 which is a variable chemical group or chain called the R group The R group confers the unique physical and chemical properties of each amino acid Side chains may be either nonpolar and hydrophobic or polar or charged and thus hydrophilic Acidic side chains contain carboxyl groups and are usually negatively charged basic side chains contain an amino group and are usually positively charged 2 List three structural differences and one functional difference between DNA and RNA There are 3 structural differences between DNA and RNA 1 DNA contains the sugar 239deoxyribose while RNA contains the sugar 239 ribose which means at the number 2 carbon on the pentose sugar there is an OH group Deoxy means there is no OH group at that position 2 in RNA the nucleotide uracil commonly replace the nucleotide thymine found in DNA The difference between Uracil and thymine is that uracil has no methyl group attached to the pyrimidine ring while thymine does have the methyl group and 3 RNA is usually single stranded not double stranded BIL 150 Chemistry m Part 2 answers pg 4 an PROVIDE THE APPROPRIATE TERM TO COMPLETE EACH STATEMENT l The most abundant protein in your body is collagen which is a type of fibrous protein 2 aromatic amino acids have side groups that contain an organic ring structure 3 denaturation refers to a protein losing its three dimensional structure 5 4 Hereditary information is stored in macromolecules called DNA and RNA BRIEFLY ANSWER EACH OF THE FOLLOWING QUESTIONS 1 The double helix structure of DNA has been compared to a spiral staircase What makes up the sides of the staircase and what the steps What holds these parts together The sides of the staircase are the sugar phosphate backbone of the individual nucleotides linked together through 339 to 539 phosphodiester covalent bonds These backbone links are formed by a condensation reaction that eliminates water Protruding from each sugar phosphate is the nitrogenous base molecules of the nucleotides adenine guanine cytosine or thymine The two chains of the staircase are held together by hydrogen bonding between the nitrogenous bases 2 What Determines Protein Conformation Protein conformation is dependent upon the interactions among the amino acids making up the polypeptide chain and usually arises spontaneously as soon as the protein is synthesized in the cell These weak molecular interactions can be disrupted by changes n pH salt concentration temperature or other aspects of the environment and the protein may denature losing its native conformation and thus its function 7 3 Can we use DNA and Proteins to monitor the progress of evolution If39so How a We can use DNA and proteins as tape measure of evolution Genes form the hereditary link between generations Closely related members of the same species share many common DNA sequences and proteins More closely related species have a larger proportion of their DNA and proteins in common This quotmolecular genealogyquot provides evidence of evolutionary relationships 4 How does a cell39s chemical and physical environment affect enzyme activity Effects of Temperature and pH The velocity rate of an enzymecatalyzed reaction may increase with rising temperature up to the point at which increased thermal agitation begins to disrupt the hydrogen and ionic bonds and other interactions that stabilize a protein39s conformation A change in pH may denature an enzyme by disrupting the hydrogen bonding of the molecule Each enzyme has a temperature and pH optimum at which it is most active 5 Why would a change in pH cause a protein to denature A change in pH will cause the weak electrostatic forces holding the protein in its speci c conformation to change Hydrogen bonds ionic bridges van der Waal39s forces hydrophilic and hydrophobic interactions may changes thereby causing the loss of some 3D structure When a native stable conformation is lost the biological activity of the protein may be lost and it is said to be denatured 6 A denatured protein may reform to its original functional shape when returned to its normal environment What does that indicate about a protein39s conformation The 3D native conformation that a protein assumes under quotits normal environmentquot is a very stables and nonenergyexpending shape While all the forces are weak molecular electrostatic forces they do assume a quotnative conformationquot at which the proteins is most energetically stable thus there must be an optimal conformation at a given environment which is quotbestquot for a protein Remember what is best in one speci c environment may not be best at some later time I 7 7 Why would transfer to an organic solvent such as alcohol cause denaturation Organic solvents such as alcohols compete for the available water of solvation which is the water that helps solubilize molecules in an aqueous environment As one increase the concentration of the alcohol less and less water is available to solvate the protein so it begins to precipitate As a matter of fact the use if organics solvents is a typical way of isolating and purifying proteins form a solution of soluble proteins BIL 150 Chemistry m Part 2 answers pg 5 Exercise 9 CONCEPT MAPS for the major macromolecules carbohydrates amp lipids Have each member of your learning community in turn ll in one of the boxes in alphabetical order If appropriate explain the concept at each lettered box CARBOHYDRATES include I 3 Hana adwri4 ITDI Salwv39r J I I 30Iifgwg dul 5I generaZfon ula R 939839 intolong joined by junction as functionas polymers 10 9 0quot energy storing structural compounds compounds Suchas suchas c My deouu I 1 good S Frw Kyar I hslyugu I I l kidVlad 1 LLFHVJ l 7 f e39g39 5 m differ due to made Of A J l I glucose I highly branched I LAAMQIS I a or 3 form glucose with polymer of glucoSe of glucose nitrogen group are inClIUde a b 39 i I hydrophobic and I L Q LVJ 5 O h Lima insoluble in water composed of 39 comp059d 0 molecules with t d 3 39 4carbon LGlicmt 1 L 9m in Lassen 15 a store e forms a may function as 35 a arm I re 1 him s g c o w ca xy group Y 1 0 393 ma7e k Ems head M e r h dro hobic I Mme I Wafd l I y 51 l bilayer forms oils kinks keep liquid solid at room at room temperature temperature Exercise 10 Short AnswerDiscussion Problems The IeVel of dif culty of each of the following problems increases and may go beyond what you have covered in lecture to this point in the course D0 each of the following questions under the guidance of your facilitator a A different member of your Learning Community is to answer each one of the following to the rest of the members of the community Give the SIGNIFICANCE not the de nition of each of these terms or phrases ie say what they do or why they are important in biology For example water the uid matrix of the cell water is the solvent for the polar molecules of a cell and determines the nal structure of many biological molecules and their interactions 1 electronegativity 2 free radicals 3 carbon 4 functional groups b Water has been described as an excellent thermal butter for cells What does that mean and what accounts for this property of water I w 44 7 l 0 v V 5 Page 6 39 Bil 150 Chemistry Workshop a ItoMt uf SENSORY PHYSIOLOGY Sensatlons amp Perceptlons sensation is an awareness of sensory stimuli in brain perception meaningful interpretation or conscious under standing of sensory data 5 Components of Sensory Physiology 1 Sensory Receptors structures that detect changes in external amp internal environment modified neurons or epithelial cells eyes ears that respond to stimuli Classes of Receptors mechanoreceptors mechanical forces 1 hair cell deflection depolarization 2 stretch receptors of muscles 3 equilibrium receptor of inner ear 4 touch receptors of skin chemoreceptors chemicals sense solutes in solvents taste smell osmoreceptors of hypothalmus which monitors blood osmotic pressure photoreceptors light eye eyespots infrared receptors of snakes etc thermoreceptors radiant energy phonoreceptors sound electroreceptors detect currents lateral line of fish electric eels etc nocireceptors pain receptors naked dendrites of skin 3202007 El 150 Sensory Physiology 4 2 Reception ability of receptor to absorb energy of a stimulus 3 Transduction conversion of stimulus energy into membrane potential a Receptor Potential change in permeability of a postsynaptic membrane is graded proportional to strength of stimulus may be amplified and may be summed 4 Transmission receptor potential transmitted via Ap39s to CNS 5 Integration processing of the frequency of receptor potentials received via summation Sensory Adaptation decreased responsiveness by receptor to continual stimulation a uniformly maintained stimulus of constant intensity is perceived as progressively weaker with time while a variable intensity stimulus of short duration is perceived as stronger SEI ISDI I Mll l l l Eldor39 1311 if u abjscl iu Int 15in 5 101 y a E M 2 IE H 39 n I E 4n 3quot l 39239 1 a l E El r l I 39 r x 7 quot39r q r I 5 JD 35 SCI 93 I39D Bil M 1m lI39l 121 131139 iicv39illlucul 11m llw i 39 tlllllrlu 3202007 Bil 150 Sensory Physiology Example of Sensory Organ the Human Eye EYE a specialized sensory organ capable of light reception in vertebrate animals formed visual images are then carried to the visual center of the brain perception Parts of a simple eye roughly spherical with opaque sides amp back with transparent front amp interior lens quotaquot amp cone cell of quot retina layer of nerve tissue of millions of light receptor cells rod cone cells transmits signals of varying light intensity fovea structure near center of retina where cone cells give max sharpness of vision optic nerve retinal cells record light images amp transmit to optic nerve which exits eyeball behind the optic disk blind spot to the Visual centers of pram sclera tough outer shell of eyeball made of dense fibrous tissue cornea stratified squamous epithelia chief refractory part of eye a ows light to pass amp aids in focusing vitreous humour transparentjellylike material helps eye keep its spheroid shape aqueous humour anterior chamber filled with a watery fluid iris muscular curtain that openscloses to regulate amount of light entering eye through the pupil opening of ir into eye 3202007 Bil 150 r Sensory Physiology Some common vision disorders correctable by eye glasses myopia nearsightedness lens39 point of focus falls within the vitreous body so that when light reaches the retina it is out of focus hyperopia farsightedness point of focus falls behind the retina out of focus astigmatism results from dereCIs in the corneal curvature rays of light don39t form a point of focus on the retina night blindness lack of chromophore retinal color blindness lack of trichromatic pigments glaucoma result of increased pressure of fluids in the eye produces defects in field of vision lead sto vision loss Optical Illusions illustrate difficulty of perception amp understanding what you see is actually what you see Seen as columns of Xs and Os rather than rows of alternating Xs and Os 3202007 El 150 Sensory Physiology another example MUSCLE PHYSIOLOGY model skeletal neuromusclarjunction see web fig an innervated muscle fiber Femqamp muscles can only contract pull Gastrocnemius 4 parts of a Muscle twitch CONTRACTION 1 latent period 5 msec time between application of AP amp initiation of contraction 2 contraction 40 msec muscle shortens amp does its work 3 relaxation 50 msec muscle elongates amp returns to original position 4 refractory period 2 msec time of recovery between stimulations recorder Summation a 2nd contraction before the lst subsides Tetany sustained contractions Fatigue under repeat stimulation contraction get feebler lactate accumulates fatigue contractions stop Shivers involuntarysummed muscle contractions which release waste heat that warms body 3202007 Bil 150 Sensory Physiology 5 2 TYPES of MUSCLE FIBERS determined both genetically and functionally based upon how fast they can produce a contractile twitch Every muscle composed of varying composition of two types TYPE I SLOW TWITCH Tonic muscle red Leg muscles slower contraction times 110 msec continuous use muscles for endurance performance marathoners good for long slow sustained contractions and prolonged performance not easily fatigued contain myoglobin red more capillary beds greater max V02 smaller in size lower 39lco39en content poor anaerobic glycolysis predominant aerobic enzymes amp aerobic metabolism higher fat content more miotchondriaBeta Oxidation high poorly formed sarcoplasmic reticulum slower release of Ca slow contractions tropinin has lower affinity for Ca 3202007 TYPE ll FAST TWITCH Tetanic muscles white Pectoral muscles faster contraction times 50 msec one time use muslces for power amp speed sprinters good in rapid contraction short time and brief performance easily fatigued no myoglobin white less capillary beds larger in size higher 39l co39en content predominant anaerobic glycolysis easily converts glycogen to lac wo 02 some aerobic capacity lower fat content fewer mito Beta Oxidation low well formed sacroplasmic reticulum quick release of Ca rapid contractions troponin higher affinity for Ca Bil 150 Sensory Physiology 5 Vertebrate Skeletal Muscle structure sarcomere repeat unit of striated muscle delimited by Zlines I band 39 clear lone around Zline isotropic A band dark region in center of sarcomere anisotropic M line mid point of sarcomere H lone clear region in cnter of sarcomer around M line SLIDING FILAMENT THEORY of Muscle Contraction d remains constant in she H Zone becomes denser I band varies in length becoming shorter Muscle relaxed extended Muscle comucllng E 9 Muscle Cell Proteins myosin 2 polypeptides forming a helix with globular end which has ATPase actlvlty amp an affinity to bind actin THICK FILAMENT Gactin globular protein which polymeriles into IN FILAMENT contains a myos ing site tropomyosin fiberlike protein which helically wraps around actin thin lament troponin globular protein which binds Ca2 Muscle Contraction Cycle amp Role of Ca review 2202007 w 1 Druensow thslologv 7 The Performance Enhancing Drugs of the Future not steroids but the introduction of artificial genes What kind of genes 1 genes for myosin type transcriptions factors which activate genes for dormant myosin isoforms for ex say an ancient type llb isoform that39s faster than any known Type II isoform of today 2 or lGFl insulinlike growth factor lGFl is a growth factor structurally related to insulin lGFl is produced in response to GH amp induces subsequent cellular activities particularly on bone growth lGFlhas autocrine and paracrine activities amp like the insulin receptor it has intrinsic tyrosine kinase activity Owing to their structural similarities lGFl can bind to the insulin cell membrane receptor Normal Muscle Cell Growth includes 1 satellite cell recruitment divide amp fuse with muscle cells 2 growth factors as lGFl promotes satellite cell proliferation 3 growth inhibition factors such as myostatin Current research HL Sweeney at U Penn has used adenoassociated virals AAV to infuse lGFl gene into muscle cells in normal mice overall size amp growth rates up 15 to 30 in mice genetically engineered to overproduce lGFl injection of AAVlFGl into one leg of lab rats with weight training program 2x increase in strength in treated leg longer period before gained strength is lost sedentary rats showed 15 increased strength quot5202007 El 150 Sensory Physiology 8 Myostatinm is a muscle inhibitory growth factor blocks muscle growth promotes atrophy and slow muscle cell growth may function antagonistically with IGFl discovered by Sejin Lee at Johns Hopkins in 1997 Belgian Blue cattle are due to defective myostatin gene defective myostatin genes considerably larger muscle mass a human case study 2004 may be useful in muscle debilitating muscle diseases as muscular dystrophy sarcopenia age related muscle loss cachexia aggressive muscle loss 39 cancer amp HIV patients myoclonus abnormal muscle contractions MW 7 Manlhs Wyeth pharmaceuticals is at work on myostatin inhibitors 0 lst drugs to date are antibodies I to myostatin and some clinical lDzm mm mm trIals are set to begIn We norm mm in MD patients 3202007 Bil150 Sensory Physiology Finis la fin alla fine al final T Aoq Extremidade KOHeu Avsluta The end 3202007 Bi 150 Sensory Physiolcgy 10 Biology 150 Fall Semester Introductory Workshop Exercise Life amp Its Chemistry PART 2 THE CHEMICAL BUILDING BLOCKS OF LIFE THE GRAND SCHEME In part 1 we learned that all matter is composed of atoms and the atoms of organisms are arranged into large complex macromolecules Life is built upon these macromolecules They store energy for later use form membranes provide structural support help control chemical reactions within the organism and store the hereditary information that is used to direct every aspect of the organism s life and is passed on to the next generation The four major categories of macromolecules are carbohydrates lipids proteins and nucleic acids 1 PROTEINS pg 7180 and ENZYMES pg 96100 De ne what a protein is and or of what it is made Being in favor of young people is not a valid answer De ne all the different functions that a protein may have NUCLEIC ACIDS pg 8085 De ne what a nucleic acid is and or of what it is made How many different kinds of nucleic acids can you name Optional Talk brie y about which you think came rst DNA or RNA amp why Some KEY TERMS in the Chemistry of Life Have one member each of your Learning Community in turn de ne one of these terms macromolecules polymer enzyme active site peptide polypeptide cofactor amino acid peptide bond conformation primary structure secondary structure tertiary structure quaternary structure disul de bridges enzyme inhibitors chaperone proteins heat shock proteins globular proteins allosteric regulation brous proteins nucleotides phosphodiester bond purines pyrimidines double helix Page 1 Bil 150 Chemistry Workshop Em 2 Match the following numbers with the appropriate statement A number may be used more Numbers 0 1 2 3 4 5 6 12 20 Statements a the number of different nitrogenous bases in DNA b the number of different chemical classes of amino acids c the number of chains of nucleotides in a DNA molecule d the number of different nitrogenous bases in RNA e the number of different amino acids found in proteins f the number of chains of nucleotides in most RNA molecules A LEARNING CHECKLIST 1 What are the building block unit of proteins How do these building blocks differ from each other 2 List three structural differences and one functional difference between DNA and RNA PROVIDE THE APPROPRIATE TERM TO COMPLETE EACH STATEMENT l The most abundant protein in your body is collagen which is a type of protein 2 amino acids have side groups that contain an organic ring structure 3 refers to a protein losing its three dimensional structure 4 Hereditary information is stored in 39 39 called Each Learning Community member in turn should brie y answer one of the following questions 1 The double helix structure of DNA has been compared to a spiral staircase What makes up the sides of the staircase and what the steps What holds these parts together What determines a protein s conformation Can we use DNA and Proteins to monitor the progress of evolution If so How How does a cell s chemical and physical enVironment affect enzyme actiVity Why would a change in pH cause a protein to denature 9959 A denatured protein may reform to its original functional shape when returned to its normal enVironment What does this indicate about a protein39s conformation 7 Why would transfer to an organic solvent such as alcohol cause denaturation of a protein Page 2 Bil 150 Chemistry Workshop Em A definition of a cell A living cell is a self contained self assembling self adjusting self perpetuating isothermal mix of biomolecules held in a 3D conformation by weak noncovalent forces which can extract raw materials precursors amp free energy from its surroundings that can catalyze reactions with specific biocatalysts enzymes which it makes that shows great efficiency amp economy of metabolic regulation that maintains a dynamic steady state far from equilibrium that can selfreplicate using the linear information of a molecule of DNA 3122007 Bil 150 Prokaryo tes 8 Viruses 1 How Cells are ORGANIZED 3 Basic Parts of a Cell 1 membrane selectively permeable inout 2 a DNA region nucleoid or nucleus 3 the cytoplasm amp its parts organelles within the three Biological Domains Eubacteria true bacteria Archaea ancient proka ryotes Eucarya modern multicellular systems 2 successful Cellular Plans of Organization 1 PROKARYOTE quotbefore nucleus includes Unicellular forms blue green algae amp bacteria primitive simple versatile common unicellular forms most successful life form 80 to 90 of total biomass of planet 2500 different species known characteristics lack membrane bound organelles genes quotnaked DNAquot no quotchromosomesquot little to no internal compartmentation size 01 to 10 um diameter arr uu 3122007 Bil 150 Prokaryotes amp Viruses Two major forms of prokaryotes exist today Archaebacteria and Eubacteria ancient amp true ARCHAEBACTERIA living archaebacteria include the extremophiles those living in extreme environments METHANOGENS coZ H2 gt CH4 HALOPHILES live in Dead Sea amp Great Salt Lake THERMOPHILES in acid hot springs deep ocean geyers ACIDOPHILES amp ALKALIPHILES acid amp base loving EUBACTERIA all lother iving bacteria modern form flagella many cause diseases Bacillis anthracis anthrax Clostridium botulinum botulism Staphylococcus aureus food poisoning Salmonella food poisoning amp typhoid many make antibiotics Streptomyces stretptomycin Penicillus penicillin CYANOBACI39ERIA are photosynthetic eubacteria Archaeanseubacteria are highly conserved living fossil forms and solve many environmental challenges problems by their chemistry and by evolving new metabolic solutions procaryotic bacteria are found in 3 common shapes cocci bacillus spirochetes J its 3 a 3 l7 i p f 90 Pnevmcw smmm humpquot 0ch Eullll SPlrocheleI 3122007 Bil 150 r Prokarvotes amp viruses current paradigm eukaryotes evolved from simpler prokaryotes Z EUKARYOTIC eu true karyon nucleus plan of multicellular organisms many internal membrane bounded organelles organelle a subcell part that has a distinct metabolic function 7 common major characteristics of eucaryotes nucleus single greatest step in evolution of animals genes in quotchromosomesquot colored bodies protein contains more DNA 1000 x more presence of organelles internal compartmentation presence of flexible cell walls allows phagocytosis presence of cytoskeleton reproduce sexually usually larger cell volume 10X greater than bacteria size 50 to 20 um diameter extensive internal membranes 2 basic types of eukaryotic cells animal metazoan heterotrophic feeder plant metaphytian autotrophic producer chloroplasts large vacuoles cellulosic cell wall 3122007 Bil 150 Prokaryotes amp Viruses Where do the VIRUSES fit obligatory intracellular parasites pathogens of made of a protein capsid capsule amp genetic material ss or ds RNA or DNA VIRION virus outside of host VIROID RNA pathogen virus wo capsid 240600 n39s Extreme viruses Viruses like extremophiles can live in Earth39s most extreme environments Origin of Viri small pieces of cell chromosomes that maintained an autonomous existence within cells Overtime these genetic elements acquired protein coats amp ability to transfer to other hosts and became infective What are PRIONS protein infectious pathogens biological activity without RNA or DNA How cause diseases as encephalopathies scrapie CreutzfeldtJacob madcow disease all are due to gt misfolded proteins Nanobes are tiny filamental structures found in some rocks and sediments smallest are just 20nm long May be crystal growth but they39 purported to hold M look similar to lifelike structures found in ALH84001 3122007 Bil 150 Prokarvo39tes amp Viruses How do we identify su bcell parts Light Microscopy resolution distance by which distinquish 2 dots 02 um killingfixing samples formaldehyde amp glutaraldehyde sectioning microtome 1 to 10 um thick selective staining types bright field phasecontrast Nomarski darkfield Olympus Provis AX 10 L F l a e orrna clrca 1958 4 3951 Camera 35 mm A apter Fi me 1 Vltleo I 9 Camera 85 m39 SpeCImen pm 3mm holder lor 9 mtclotome Flttevs Evevleces Analyzels a Retardant th Plates New lnulcator LEDS came l lllumlnator 39 Photomlmgmnh Controller 1 P CDWD IEr Sections are cut on an ultramtcrotoma g wllh a glass or diamond knlle i e The secllons are oated all the edge nl the knlle unlo lhe surface 0 a water trough Condenser Fllters Focus Electron Microscopy resolution 02 nm 3D Orange Bowl cross section TEM Transmission SEM Scanning see figure examples FfEM Freeze fracture Size relationships of parts Cell Isolation amp Culture HeLa cells Homogenization Fractionation amp Centrifugation 3122007 Bil 150 Prokalyotes 8L Viruses Major Eukaryotic sub cell ORGANELLES NUCLEUS envelope chromatin nucleolus nucleoplasm MITOCHONDRIA perimitochondrial space cristae matrix CH LOROPLAST perichloroplast space thylakoids stroma RIBOSOME small unit large unit polysome ENDOPLASMIC RETICULUM smooth amp rough GOLGI BODY sided cis amp trans endomembrane pathway LYSOSOME hydrolytic enzymes MICROBODIES peroxisome amp glyoxysome CYTOSKELETON microfilaments microtubules intermediate filaments CENTROSOME centriole basal body flagella cilia INTRACELLULAR JUNCTIONS tightjunctions desmosomes gapjunctions plasmodesmata PLANT CELL VACUOLE surrounded by membrane stores waste balance osmosis CELL MEMBRANE surrounds cell amp regulates what gets inout 3122007 Bil 150 Prokaryotes 8 Viruses
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