Foundations of Bio 1 Unit 1
Foundations of Bio 1 Unit 1 BIOSC 0150
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12 Cell Theory Monday August 25 2014 622 PM Cell theory A organisms are made of cells and all cells come from preexisting cells What are organisms made of Where do they come from 1665 Robert Hook creates crude microscope observed individual units within oak dubbed quotcellsquot due to resemblance to prison cells Leeuwenhoek created much more powerful scopes soon after observed pond life blood sperm Two hypothesis Cell theory was in direct opposition of widely held quotspontaneous generationsquot in which it was thought cells would arise of their own accord from nutrient rich mediums AII from cells theory was hypothesis at time Experiment to settle the question Louis Pasteur and the swan neck Pasteur s Test if f Spontaneous Generatiun 39l r Eurml Heel 39 is Baum Emil is Euilled rutlr Remains Free If Mlnmur i lisms lilitmnr39ganism Eruw ll Emlll39i Results supported all from cells theory Module 1 Page 1 YOU SHOULD BE ABLE TO DESCRIBE THE EVIDENCE THAT SUPPORTED THE PATTERN AND THE PROCESS COMPONENTS OF CELL THEORY Cell Highly organized compartment bounded by thin flexible membrane plasma membrane contains concentrated chemicals in aqueous solution Reproduce thru divisionfission 1 5 Dom Biolo YOU SHOULD BE ABLE TO EXPLAIN 1 THE RELATIONSHIP BETWEEN A HYPOTHESIS AND A PREDICTION 39 g AND 2 WHY EXPERIMENTS ARE A CONVINCING WAY TO TEST PREDICTIONS Monday August 25 263114 654 PM Hypothesis testing 1 State the hypothesis as precisely as possible and list the predictions it makes 2 Design an observational or experimental study that is capable of testing those predictions Science Formulate hypotheses and finding evidence that supports or conflicts with those hypothesis Why do Giraffes have long necks An introduction to hypothesis testing Food competition Hypothesis neck length variable among giraffes neck length is heritable giraffes feed high in trees during dry season when food is scare and threat of starvation is high Characteristics of Good experimental Design Critical to include control groups Experimental condition must be as constant or equivalent as possible HOWEVER giraffes do not fully extend neck during feeding so much of neck is superfluous Repeating the test is essential Sexual competition hypothesis Giraffes mate ear round and males fight each other for mates longer neck can bash down opponents from farther away Hypothesis and Predictions Hypotheses are proposed explanations that make testable predictions Predictions describe observable outcomes of particular conditions Module 1 Page 2 21 Atoms ions and molecules The building blocks of chemical evolution Monday August 25 2M4 721 PM Four types of atoms hydrogen carbon nitrogen and oxygen make up 96 percent of all matter found in organisms today How did elements evolve into the more complex substances found in living cells What is the physical structure of the hydrogen carbon nitrogen and oxygen atoms found in living cells What is the structure of the simple molecules water carbon dioxide and others that served as the building blocks of chemical evolution Basic Atomic Structure 5 PT D EDII39IS Proton positive charge 1 39 5 Emml39l Neutrons electrical neutral Electrons negative charge 1 Protons cannot vary it will have a different atomic number thus a different element is made Neutrons can vary known as isotopes Q Enemmn When there is an imbalance of protons and neutrons a radioactive isotope is created V Nucleus will decay and one of the neutrons will change into a proton proton o r lIEiLiilll ll l Mass of protons neutrons and electrons is so small that it is measured in Daltons Neutron and Proton have mass of 1 Dalton CarloDin aftDim To understand how atoms involved in chemical evolution behave Focus on how electrons are arranged around the nucleus Polarcwnlrntlhnm Nunnnlnrtwa enlzbnnd Manama camera mu Electrons move around the atomic nuclei in specific regions called orbitals Each orbital can hold up to two electrons Orbitals are grouped into levels called electron shells Electron shells are numbered 123etc to indicate relative distance to the nucleus smaller is closer Each electron shell can hold a specific number of orbitals shell with one orbital has 2 electrons whereas shell with four orbitals has 8 electrons Electrons fill the innermost shell first and then proceed further away The outermost shell of the atom contains all the valence electrons The amount of unpaired electrons is referred to as an atoms valence Covalent Bonding An atom is most stable when all of its electrons are paired one of the ways to do this is by chemical bonding attractions that bind atoms together An attraction where atoms share one or more pairs of electrons is called a covalent bond Substances held together by covalent bonds are called molecules Electronegativity of four most common elements in organisms OgtNgtC2H Nonpolar and polar bonds When electrons are shared equally the charge is not changed and a nonpolar covalent bond is formed When electrons are not equally shared a polar covalent bond is formed This happens because some atoms hold onto electrons in covalent bonds more tightly than other atoms electronegativity 39 Electronegativity is judged by 1 amount of electrons in valence shell 2 the distance between valence shell and nucleus closer the shell the higher the electronegativity up and to the right on periodic table excluding rightmost column as those have full shells As a result of the electron spending more time near more electronegative atoms and less time away from less electronegative atoms 6 is assigned Module 1 Page 3 Ionic Bonds Ionic bonds are formed when an electron is completely transferred from one atom to another This occurs because it gives resulting atoms full outermost shells As a result of the electron lossgain a full charge is now either gained or lost by the participating atoms A positive ion is called a cation and a negative ion is called an anion Representing Molecules Module 1 Page 4 was LIT gainolz39 alle mn If 39a clinchmum an K It nith In Iiu r alum tnruilrni 5 an li39ll39l millw hf I lismg Iri nilrl il1 L39III1 Ir El39j39 HHII IIIIQ am lll 39t lrl ll aringII 22 Tuesday August 11 Properties of Water and the Early Oceans rib Water is vital because it is the universal solvent an agent for dissolving substances into a solution Why Both of the 0H bonds are polar owing to 0395 high electronegativity as a result 0 has a partial negative and H has a partial positive The molecule is bent so the negative charge sticks away from the positive charge giving it overall polarity Because of Waters polarity almost any charged or polar object can dissolve in water these are said to be quothydrophilicquot In contrast substances that are not polar and uncharged cannot dissolve in water and are said to be quothydrophobicquot Although hydrogen bonds are not as strong as ionic or covalent bonds they are extremely important simply due to the sheer number of hydrogen bonds between water and hydrophilic substances Cohesion adhesion and surface tension Cohesion is attraction between like molecules water is cohesive it stays together because of hydrogen bonds that form between individual molecules Adhesion is attraction between unlike molecules usually between a liquid and solid Water adheres to surfaces that have any polar or charged components Surface tension is when water molecules at the top of the surface have no molecules to bond to above them so they exhibit stronger attractive forces to molecules next to them resulting in an important consequence Water resists any force that increases its surface area Role of water in AcidBase reactions H20 can be broken down into H hydrogen ions protons and OH hydroxide ion but in reality protons do not exists by themselves thus the disassociation of water is more accurately described as H20 H20 H30 OH One of the molecules of water has accepted a proton whilst another has given up a proton Substances that give up protons during chemical reactions are called acids Substances that acquire protons during chemical reactions are called bases Most acids remain as acids and most bases remain as bases but water can be both acid and base Every acidbase reaction requires a proton donor and acceptor an acid and base Strong bases will readily acquire protons when they react with water and strong acids will readily give up protons Adding an acid to a substance increases the concentration of protons Adding a base to a substance decreases the concentration of protons Molarity is that number of moles present in 1 liter of a substance pH ogH Hquot antilog pH 10quotpH Buffers protect against damaging changes in pH Compounds that minimize changes in pH are called buffers because they reduce the impact of adding acids or bases on the overall pH of the solution Module 1 Page 5 IF YOU UNDERSTAND HOW THE WATER39S STRUCTURE MAKES HYDROGEN BONDING POSSBILE YOU SHOULD BE ABLE TO 1 DRAW A FICTIONAL VERSION THAT SHOWS WATER NOT BENTLINEAR WITH PARTIAL CHARGES ON THE OXYGEN AND HYDROGEN ATOMS AND 2 EXPLAIN WHY ELECTROSTATIC ATTRACTIONS BETWEEN SUCH WATER MOLECULES WOULD BE MUCH WAEKER AS A RESULT Water is denser as a liquid than as a solid In ice each water molecule participates in four hydrogen bonds these result in a crystalline structure to form which is highly open resulting in low density When heated the bonds break and the open structure collapses making liquid water much denser than frozen water Why is this important Since ice floats above water it provides an insulating layer to water instead of sinking to the bottom and remaining frozen Without this feature earth39s oceans would have frozen long ago before life had a chance to start Water has a high capacity for absorbing energy Specific heat is the amount of enerygy required to raise the temperature of 1 gram of a substance by 1 degree Celsius Water has a high specific heat because it requires that the hydrogen bonds be broken before the molecule starts moving faster As a substance increases in overall polarity the ability to make hydrogen bonds the specific heat rises Bleach Snapy water Amrrlonia solution If ill I rT39 gritm 3 33quot I39ll soda TamI wal I IIitIIIr ed In ate Jri39u EIEIEIL CIDI39DE IquotC39I jLI iLI Lt39ai39ge Jur EI11iI39III39JICE UEStrII EIIZIU 23 Chemical reactions energy and chemical evolution Tuesday August 26 2M4 234 PM Proponents of chemical evolution contend that simple molecules participated in chemical reactions that led to more complex organic molecules Two environments where these reactions are thought to have occurred are The atmosphere which was probably dominated by gases ejected from volcanoes Water vapor carbon dioxide and nitrogen are the dominant gases ejected by volcanoes today small amount of molecular hydrogen and carbon monoxide may also be present Deep sea hydrothermal vents where extremely hot rocks contact deep cracks in the sea floor In addition to gases such as CO2 and H2 certain deep sea vents are also rich in mineral containing reactive materials such as nickel and Iron When gases like CO2 N2 H2 and C0 are put together and allowed to interact on their own very little occurs They do not suddenly link together to create large complex substances like those found in cells Instead their bonds remain intact What is energy Energy is the capacity to do work it is either stored as potential or as an active motion When stored in chemical bonds potential energy is called chemical energy Kinetic energy is energy of motion the transfer of thermal energy is called heat What makes chemical reactions spontaneous Reactions are considered spontaneous when they can proceed on their own without any continuous external influence such as added energy Reactions tend to be spontaneous when the product molecules are less orderly than the reactant molecules Reactions tend to be spontaneous when the products have lower potential energy than the reactants If the electrons in the reaction products are held on more tightly higher electronegativity Module 1 Page 6 How do chemical reactions happen The initial or reactant molecules are shown on the left and the resulting reactions the products are shown on the right The physical state of each reactant and product is indicated as gasg liquidl solids or in an aqueous solutionaq Chemical equilibrium is when the quantities of products and reactants remains constant 2nd law of thermodynamics Entropy disorder always increases in a closed system Physical and chemical processes proceed in the direction that results In increased entropy and lower potential energy 24 Investigating Chemical Evolution Approaches and Model Systems Monday September 1 ZQM 123 PM To probe the different kinds of reactions that may have set chemical evolution in motion scientists use either a quottop downquot method or the quotbottom upquot method Top Down Researchers examine chemistry that is shared throughout the tree of life Such reactions are prime candidates for being involved in the chemical evolution that led up to LUCA Last Universal Common Ancestor Bottom up Primary focus is on the small molecules and environmental conditions that were present in early earth Researchers focus on reactions that could have been possible with what was available at the time without regard to modern cells These approaches have been used to investigate two different model systems The pre biotic soup model Proposed certain molecules were synthesized from gases in the atmosphere or arrived via meteoroids and condensed with rain into the oceans The process would result in an organic soup that allowed for the construction of larger more complex molecules The surface metabolism model Suggests that dissolved gases came in contact with minerals lining walls of deep sea vents and formed more complex organic molecules Early origin of life experiments Created a miniature version of ancient earth once he began adding pulses of energy lightening to the experiment found that larger more complex organic compounds had formed hug Water eeper quot t I tmespherie I quotUteenltquot sempertmsent C Eieeser empenmem ceels gas i quot quott ii The eceeequot is sampled and Heat its cempesiten analyzed Effect on sunlight Because earth was not protected by a layer of 03 ozone molecules were bombarded by high energy protons that could break up protons and create free radicals Created the high amount of energy to create formadahylde which was used in ancient chemical reactions to create more complex compounds This supports the theory that high potential energy compounds could have accumulated in the quotprebiotic soupquot oceans and led to chemical evolution however dilution of the compounds would have stopped this The surface metabolism model corrects this A layer of reactive minerals deposited on the deep sea vents would have attracted the diluted chemicals and would have created chemical evolution Module 1 Page 7 Free Radicals Atoms with unpaired electrons in their valence shell making them highly reactive 25 The importance of organic molecules Monday September 1 2014 248 PM Almost all molecules found in organism contain carbon all carbon containing compounds all called quotorganicquot Carbon has great importance in biology because it has 4 valence electrons which allows for 4 bonds which provides a limitless array of possibilities Functional Groups Carbon gives the skeleton for which molecules get their overall shape uNETEGE39MLGHQUP Fillinl39urm AWEDFEDMFEUHDE EMMFE ii iii ili 39m l Esau News HECEEJE E l l E thanel iiht39 drug Elf alcoholic beverages G H H 7 at 7 a l amongi H L hidelurks I int R is I 5quot H H H Nominal I39l H I I i I Fit E F itemize iiii I il i H Miriam at 20 Miami H C H IL Eri bazy iii acids H it DH Ell liirtl39 l l li Eienuedl acetic acid 39quot39 ti5 imd oi i Hagar lIi iimm R R quotTlH illmilitia a quotH H H inm mmredl l nIEE J Glycine tan ammo t Ill ill hilii t E iii Tinms H fT lili Fl iii Elemamped anal ill 1le ill ll l Fli mpl iah39 Ft D E agrant ll l ia It ill ii H Glyt urt il FFIIEUHHHWE 39 fit It39l39IEI Fa i39rib lliei theta ban mew 1E WIII39LEI L39l it luminarian I Lluua Ina outth 39 quot 15er 31 L143 ErrPratt rd rlhu ll mirl incl Irr39 m ltaigzf pitquotand 51i r33 HmmmL Jam aim and mlmrr ure ragim m hale phgir ig pg W Module 1 Page 8 31 Amino Acids and Their Polymerization Tuesday Septen lber Z 14 Theory of Chemical Evolution Step 1 Began with production of small organic compounds from reactants such as H2 N2 NH3 and C02 Step 2 These small simple organic compounds reacted to form mid size molecules such as amino acids nucleotides and sugars Step 3 Mid sized building block molecules linked to form the types of large molecules found in cells today including proteins nucleic acids and complex carbohydrates Each of these large molecules is composed of distinctive chemical subunits that join together Proteins are composed of amino acids nucleic acids are composed of nucleotides and complex carbohydrates are composed of sugars Step 4 Life became possible when one of these large complex molecules acquired the ability to replicate itself By increasing in copy number this molecule would then emerge from the pool of chemicals At that point life had begun chemical evolution gave way to biological evolution Most molecules in your body are composed ofjust 20 different amino acids The Structure of Amino Acids All amino acids have the same central core structure a central carbon alpha carbon bonded to four Non ionized groups 1 H a hydrogen atom ll 2 NHz an amino functional group H 3 COOH a carboxyl functional group Ham 3 If 4 A distinctive R group side group h R H In pH 7 the concentration of protons causes the amino group to act as a has eand it gains a proton thus making in NH3 The carboxyl group in contrast is highly electronegative because of its two oxygen atoms and loses a proton to form COO Ionized Amino Acid base side chains distinguish the The Nature of Side Chains The properties of amino acids vary because of the various R groups acids into four basic groups acidic basic uncharged polar and nonpolar How to determine type of amino acid Functional Groups Affect Reactivity 1 Does the side chain have a negative charge If so it has lost a proton so it must be acidic Several of the side chains contain carboxyl sulfhydryl hydroxyl or amino functional groups under the right conditions these groups can participate in chemical reactions Other groups contain mostly hydrogen an carbon and are not reactive and instead their effects on the proteins are based more on size and shape 2 Does the side chain have a positive charge If so it has taken a proton so it must be a base 3 If the side chain is uncharged does it have an oxygen atom If so the highly electronegative oxygen will result in a polar covalent bond and thus is uncharged polar The Polarity of Side Chains Affects Solubility Nonpolar side groups lack charged or highly polar groups capable of forming hydrogen bonds with the water and a result are hydrophobic Instead of dissolving within water they tend to coalesce Polar or charged side chains interact readily with water and are hydrophilic These dissolve in water easily How Do Amino Acids Link to Form Proteins Condensation Makes sense because it increases entropy and is favorable energetically The Peptide Bond When a bond between the carboxyl group of one amino acid and the amino group of another it is a peptide bond The C N bond is unstable compared to the linkages of other macromolecules because the valence electrons in the nitrogen are partially shared Module 1 Page 9 After linked amino acids are referred to as quotresiduesquot to differentiate them from free amino acids Although the bond itself cannot rotate the single bonds on either side can When fewer than 50 acids are linked it is called a quotoligopeptidequot anything larger is a quotpoly peptide Module 1 Page 10 32 What Do Proteins Look Like Wednesday September it mm 122 AM Proteins can serve diverse function in cells because they are diverse in size and shape as well as in the chemical properties of their amino acid residues No matter how large a protein is it can be broken down into 4 subdivisions Primary Structure Unique sequence ofamino acids in a protein Fundamental to the higher levels of a proteins structure Secondary Structure Created by hydrogen bonding between components ofthe peptidebonded backbone CO group of one residue carries partial negative charge to due electro negativity of Oxygen NH group has partial positive because electronegativity of Nitrogen Hydrogen bonding between the two groups stablize the secondary structure and create one of two possible structures 0 Alphahelix o Betapleated sheet Which one if either forms is dependent on the molecules primary structureprimarily the geometry and properties ofthe amino acids in the sequence Although each hydrogen bond is relatively weak the large number of them makes the secondary structure highly stable Tertiary Structure Most of the overall shape the tertiary structure is the result from interactions between Rgroups with other Rgroups and with the backbone Unlike 2ndary groups where hydrogen bonds are the only type on interaction occurring tertiary structures have 5 important interactions 1 Hydrogen bonding i Between opposite polar Rgroupsbackbone 2 Hydrophobicinteractions i Water interacts with the hydrophilic side chains and forces the nonpolar side chains to coalesce into globular mass Causes surrounding water to form more hydrogen bonds increasing the stability of their own interactions 3 Van Der Waals interactions i Once hydrophobic side chains are close to each other their association is further stabilized by electrical interactions van der Waals ii If one nonpolar molecule gets close to another a minute partial charge on one will induce an opposite charge on the other molecule causing an attraction iii Although weak relative to covalent bonds or even hydrogen bonds a large number of these can significantly increase stability 4 Covalent Bonding disulfide i Can form between the side chains of two cysteines through a reactions between the sulfhydryl groups ii Frequently referred to as bridges because they create strong links between distinct regions ofthe same polypeptide or two separate polypeptides 5 Ionic Bonding i Forms between groups that have full and opposite charges In part tertiary structure also depends on the presence of alphahelices and betapleated sheets depends on both primary and secondary structure Quaternary Structure The first three levels involve individual polypeptides but some proteins contain multiple polypeptides that interact to form a single structure Cells all contains macromolecule machines Module 1 Page 11 L 1quot 39Il I I C c I 8 Hquot 039C Hplealed sheet N a u helix 39wclt The Four Levels of Protein Structure a unmlq murmu C JN I wardIvy unmure ounpculme gunman rum hon C urinary armmm D qumunwy a hut u Sumnuy 01 me Mu lone 0 amen group 7 N 0 I Meme arc91 umrlure uunq Pm voom u an CIJWQ 0 Groups of proteins assembled to carry out tasks I ribosomes Module 1 Page 12 41 What is a Nucleic Acid Saturday September 6 2014 353 PM Nucleic acids are polymers created by monomers called nucleotides They are made of o A phosphate group 0 A five carbon sugar I Ribose in RNA I Deoxyribose in DNA 0 A Nitrogenous base I Cytosine I Guanine I Adenine I Thymine I Uracil RNA replaces Thymine willquot Wy rung b an deoxywihngh M Ribonudum L you 39 39 quothm WWW H 11 mmmanmmrcaumnqdm 55 uooiaedm h Polymerization requires an energy source Polymerization reaction is not spontaneous requires input energy The addition of two phosphate groups raises the potential energy of the now quotactivatedquot nucleotide and makes polymerization possible ATP Could Nucleic Acids Have Formed in the Absence of Cellular Enzymes Yes Researchers have been able to incubate RNA molecules up to 50 nucleotides long by using tiny mineral particles when added with heat and lipids up to 100 nucleotides long Module 1 Page 13 RNA World Hypothesis Many researchers believe that life began as an RNA molecule RNA world hypothesis Chemical evolution led the creation of an RNA molecule that could replicate itself Chance errors in replications created variations that would undergo natural selection 0 At this point chemical evolution had ended and biological evolution had begun Ribo nucleotides v deoxy ribonucelotides These two sugars differ by one oxygen 0 There is only an H on the 2 carbon of deoxyribose as opposed to the OH in ribose They also differ in the types of nitrogenous bases Broken in Purines and Pyrimidines Purines are linked together by NINE atoms and consist of adenine and guanine Pyrimidines are created with 6 atoms and are composed of Cytosine Thymine and Uracil How do nucleotides polymerize to form nucleic acids Form when nucleotides polymerize Involves the formation of a bond between a hydroxyl group on the sugar component of one nucleotide and the phosphate group of another nucleotide This link is called a phosphodiester bondlinkage DNA and RNA strands are directional One end has an unlinked 539 phosphate and the end has an unlinked 339 hydroxyl meaning the groups are not linked to another nucleotide Written in the 539 gt 339 direction Why do added phosphate groups raise he energy content of a molecule Since phosphates are negatively charged linking two or more together creates strong repulsive forces as a result these bonds carry a high amount of potential energy which can be harvested for other chemical reactions Addition of one or more phosphate groups make otherwise nonspontaneous reactions possible 42 DNA Structure and Function Saturday September 6 263114 527 PM DNA and RNA molecules have a sugarphosphate backbone created by phosphodiester linkages and a sequence of any four nitrogenous bases that extend from it What is the nature of DNA39s secondary structure Early Data Provided Clues Watson and Crik knew that molecule had a sugarphosphate backbone Chargaff established that o The number of purines in a given DNA molecule is equal to the amount of pyrimidines o The number of A39s and T39s are equal and the number of 6395 and C39s are equal 0 Xray crystallography showed that three distances between groups of atoms I 34nm 2nm 34nm suggested that the molecule was helical or spiral in nature DNA Strands Are Antiparallel Watson and Crik analyzed the geometry and size of deoxyribose phosphate groups and nitrogenous bases The bond angles and measurements suggested that 2mn represented the width of the helix and that 34nm was the distance between bases stacked in a spiral But how did this account for Chargaff39s rule as make sense of the 34nm measurement a number 10 times the distance between pairs They arranged two strands of DNA sidebyside and running in opposite directions one strand ran in the 539gt339 direction while the other was oriented 339gt539 If the strands are antiparallel to form a double helix the coiled sugarphosphate backbone is on the outside of the spiral and the nitrogenous bases on the inside For the bases from each backbone to pit the 2nm width of the spiral they have to form purine pyrimidine pairs 0 The pairing allows hydrogen bonds to form between specific purines and pyrimidines AT GC A T and GC bases were said to be complementary Two hydrogen bonds from when AT pair and three form when GC pair in contrast AC and GT pairs allowed no or only one hydrogen bond The Double Helix The shape of the structure keeps the hydrophobic bases on the inside and the hydrophilic backbone on the outside the negatively charge phosphate groups interact with water Stabilized by hydrophobic interactions n the interior and bonding between AT GC DNA Functions as an InformationContaining Molecule In all organisms that have been observe to date from tiny bacteria to gigantic redwood trees DNA carries the information required for the organisms growth and reproduction DNA39s primary structure one strand serves as a template for the synthesis of a complementary strand Module 1 Page 14 Step 1 Heating or enzymecatalyzed reactions can cause the double helix to separate Step 2 Free deoxyribonucelotides form hydrogen bonds with complementary bases on the original strand of DNA template strand As they do their sugarphosphate groups create phosphodiester linkages to create a new strand complementary strand Note the 539gt339 directionality of complimentary strand is opposite that of the template strand Step 3 Complementary base pairing allows each strand of a DNA double helix to be copied exactly producing two identical daughter molecules s DNA a Catalytic Molecule The DNA double helix is highly structured It is regular symmetric and held together by hydrogen bonding hydrophobic interactions and phosphodiester linkages In addition it has few functional groups which can participate in reactions It is very resistant to degradation The orderliness and stability that make DNA such a dependable information repository also make it extremely inept and catalysis Because RNA has a 239 hydroxyl group it is much more reactive and this is why scientists believe that life started out as RNA Module 1 Page 15 43 RNA Structure and Function il U3 f The first living molecule would have needed to perform two key functions Carry information Catalyze reactions that promoted its own replication How Structure Structurally RNA differs from DNA Primary Structure H Like DNA RNA has a primary structure consisting of sugarphosphate backbone formed by L5 r phosphodiester linkages and extending from that backbone a sequence of four types of nitrogenous bases But there are two significant differences 1 The sugar in the sugarphosphate backbone of RNA is ribose not deoxyribose a The hydroxyl OH group on the 239 carbon of ribose is much more reactive than the hydrogen atom on the 239 carbon of deoxyribose 2 The pyrimidine base thymine does not exists in RNA Instead RNA contains the closely related pyrimidine base uracil When the RNA folds in certain ways the OH group can attack the phosphate linkages between nucleotides which can generate a break in the sugarphosphate backbone While this makes RNA much less stable than DNA it can also support catalytic activity by the molecule E39Hydrow E39Deuw Secondary Structure Types of Secondary structures quot Secondary structure results from complementary base pairing AU GC If the section where the fold occurs includes However the base pairing occurs on the same strand rather than forming hydrogen bonds with unpaired bases then stemandloop configuration complementary bases on another strand like DNA results in a Hairpin this is only one of several types of RNA secondary structures When the strand folds over and aligns with the ribonucleotides on the other part ofthe same stride the two sugarphosphate strands become antiparallel In this configuration hydrogen bonding between bases makes a stable double helix Tertiary Structure RNA molecules can also have tertiary structure which arises when secondary structures fold into more complex shapes As a result there are very different overall shapes and chemical properties RNA molecules are much more diverse in size shape and reactivity than DNA molecules Structurally and chemically RNA is the intermediate between the simplicity of DNA and the complexity of proteins RNA39s Structure Makes It an Extraordinarin Versatile Molecule RNA is an intermediate in terms of function as well It cannot archive information nearly as well as DNA but it can perform all the vital functions of information processing It cannot catalyze as many reactions as proteins can but the ones it can catalyze are particularly 39it39 t quot 39 39 quot W x iv important RNA Is an InformationContaining Molecule Step 1 Complementary bases attach to the original strand of RNA Step 2 The Complementary bases polymerize together to form a complementary strand Step 3 After heating or catalyzed reactions break apart the original strand and the complimentary exist g independently of each other I H I A Step 46 Steps 13 are now repeated using the complementary strand as the template and the end 39 product results in a duplicate of the original strand 39 I t 9 RNA Can Function as a Catalvtic Molecule 3 Copy and emulate 6 mayquot 1 Module 1 Page 16 PIUUUUL ICJUILJ III a UUPIIUULC UI LI IC UI ISIIIUI JLIUIIU RNA Can Function as a Catalytic Molecule Although RNA is not as more restricted then proteins in the scope of its reactions because it only has 4 amino acids as opposed to proteins 20 it has a degree of structural and chemical complexity and is capable of catalyzing a number of chemical reactions Ribozymes catalytic RNA owe their catalytic properties to their three dimension quotactive sitesquot that mimic proteins and can promote reactions Module 1 Page 17 51 Sugars as monomers Monday September 1 263114 32 3 PM The term quotcarbohydratequot or sugar encompasses the monosaccharides small polymers oligosaccharides and the large polymers polysaccharides The molecular formula for many of these molecules is CH 20n where n represents the number of quotcarbohydratequot groups Sugars as monomers Important not only for energy but also because they contain some of the molecular building blocks for larger compounds The presence of carbonyl groups along with multiple hydroxyl groups gives sugars an array of reactive and hydrophilic functional groups Monosaccharides and Chemical Evolution Many ways in which monosaccharides were synthesized in prehistoric earth When formaldehyde molecules are heated in a solution they react with one another to form almost all the pentose39s and hexoses In addition three carbon ketoses and a wide array of compounds related to sugars were found on a meteorite that struck earth leads researchers to believe that sugars are synthesized on dust particles and other debris in interstellar space Synthesis of sugars could have also been catalyzed in deep sea hydrothermal vents Researchers maintain that one or more of the following methods led to accumulation of monosaccharides in the early oceans Module 1 Page 18 Aldose v Ketose Although they have the same chemical formula C3H503 their molecular structures are different In an aldose the carbonyl group is at either end In a ketose the carbonyl group is within the carbon chain H H Ell w Ill Haul E39EIH HEIlEEIH I I aim aldose 1quot Ketose The reason there can be so many variations of monosaccharides is because the changes in structure can change the function of the molecule 52 The structure of polysaccharides Monday September 1 2014 531 PM Simple sugars can be covalently linked into chains of varying length complex carbohydrates Monosaccharides polymerize when a condensation reaction ours between two hydroxyl groups resulting on a covalent interaction called glyosidic linkages The inverse reaction hydrolysis cleaves these linkages Starch A storage polysaccharide in plants Starch consists of entirely alphaglucose monomersjoined by glyosidic linkages The bent linkages between C1 ad C4 cause a coiled shape Actualy composed of two polysaccharides one is an unbranched molecule called amylose which contains only alpha 14 glyosidic linkages The other is a branched molecule called amylopectin Branches occur between C1 carbon on one strand and C6 carbon on another strand Occurs in about 1 of 30 monomers Glycogen A highly Branched Storage Polysaccharide in Animals Performs the same storage function that starch does in plants Polymer of alpha 16 glyosidic linkages glucose monomers Identical to starch except branch occurs in every 1 of 10 units instead of 30 Cellulose A Structural Polysaccharide in Plants Major component of cell walls in plant cells Polymer of betaglucose monomersjoined by beta 14 glyosidic linkages Every monomer is flipped in relation to the monomers adjacent to it this is important because it creates a linear molecule as opposed to the helix in starch allows multiple hydrogen bonds to form in parallel lines that are joined by hydrogen bonds Chitin A Structural polysaccharide in Fungi and Animals Stiffens the cell walls of fungi and most importantly the exoskeleton of insects and crustaceans Similar to cellulose but instead of glucose monomers the monosaccharide involved is called N acetylglucosamine NAG These NAG monomers are joined by beta 14 glyosidic linkages just like cellulose every other monomer is flipped Like the glucose in cellulose hydrogen bonds in adjacent strands forming a tough sheet Peptiodoglycan A structural polysaccharide in bacteria The equivalent of cellulose in plants Long backbone of two monosaccharides that alternate with each other and are linked by beta 14 glyosidic linkages A short chain of amino acids is attached to one of the monosaccharides When peptidoglycan aligns the amino acids bond together serving the same purpose as the adjacent hydrogen bonds in cellulose an chitin Polysaccharides and Chemical Evolution Although Cellulose and Chitin are probably the two most common organic compounds on earth they likely played little to no role in the origin of life This conclusion is supported by several observations No plausible mechanism exists for the polymerization of monosaccharides under condition that prevailed early in Earth39s history To date no polysaccharide has been discovered that can catalyze polymerization reactions The monomers in polysaccharides are not capable of complementary base pairing Module 1 Page 19 53 What do carbohydrates do Tuesday September 2 26314 1158 PM Serve as substrate for synthesizing more complex molecules RNA contains 5 carbon sugar ribose DNA contains modified sugar deoxyribose Frequently furnish the raw carbon skeletons that are used as the building blocks in the synthesis of important molecules Also indicate cell identify and store chemical energy Carbohydrates can provide structural support Cellulose chitin and peptidoglycan are key structural components they form fibers that give cells and organisms strength and elasticity Are durable Very few organisms contain the enzymes capable of hydrolyzing cellulose chitin and peptidoglycan The strong interactions between strands consisting of beta 14 glyosidic linkages exclude water and the fibers tend to be insoluble The role of carbohydrates in cell identity Polysaccharides can have enormous amounts of diversity and as a result can be used as a badge to identify types of cells via their unique structure Glycoproteins on the membrane of a cell identify it Carbohydrates and energy storage Photosynthesis use C0 H20 Sunlight CHZOn 02 the electrons in CO bonds in Oxygen have low potential energy because of the high electronegativity of Oxygen the electrons in CH and CC bonds in carbohydrates are shared equally and thus have a high potential energy Enzymes Hydrolyze Polysaccharides to release glucose Polymerize via alpha glyosidic linkages as opposed to structural beta linkages of structural carbohydrates Catalyzed by phosphorylase which is stored in many cells to break down glycogen to produce glucose on demand Amylases are enzymes that break down alpha linkages to create glucose subunits Module 1 Page 20 Carbohydrates are like the water that piles up behind a dam ATP is the electricity generated in the dam that is used to power your home Carbohydrates store the energy and ATP makes that energy useful to the cell 61 Lipid Structure and Function Saturday September 6 ZQM 1249 PM I I I Why are lipids hydrophobic Since they are significantly made of long chains of C H bonds hydrocarbons they do not have partial charges owing to the Lipids are the foundation of a cells membrane approximate equal electronegativity of C and H Lipid is a term used to describe carbon containing compounds that are found in organisms that are largely nonpolar or hydrophobic meaning they do not dissolve readily into water Bond Saturation is an important aspect of Hydrocarbon structure In the double bond atoms are locked into place and cannot rotate freely as they do in single bonds As a result double bonds between carbon atoms create quotkinksquot in otherwise straight hydrocarbon chains Hydrocarbon chains that consist of only single bond C C are called saturated if one or more double bonds exist in the hydrocarbon chains then they are unsaturated A Look at Three Types of Lipids Found in Cells Fats Also known as tri glycerides 3 fatty acids linked to a three carbon molecule called glycerol Primary function is energy storage When made of polyunsaturated fatty acids they form oils Steroids Distinguished by four ring steroid rings present in all steroids Differ from different functional groups and side groups attached to carobs in steroid rings What is amphipathic Phospholipids When a molecule has both hydrophobic and Contains a glycerol that is linked to a phosphate group and two hydrocarbon chains of either hydrophilic regions isoprenoids or fatty acids The phosphate is also bonded to a small organic molecule that is charged or polar Phospholipids containing fatty acids are found in the domains Bacteria and Eukarya Phospholipids containing isoprenoid chains are found in domain archaea Crucial component of cell membrane The Structures of Membrane Lipids Lipids must be amphipathic in order to form membranes Essential to the creation of membranes One side interacts with water whereas one does not Were Lipids present during chemical evolution Fatty acids could have been synthesize from H2 and C02 via reactions with mineral catalysts under conditions thought to be present in prebiotic hydrothermal vent systems Could have also been brought on meteorites Module 1 Page 21 62 Phospholipid Bilayers Saturday September 6 2014 245 PM Hydrophilic heads and hydrophobic tails align in two forms Micelles tiny droplets when heads face water and form hydrogen bonds and tails interact with each other in the interior away from water tend to form from fatty acids or other simple amphipathic hydrocarbon chains d Lipid bilayer 4 39 J Two sheets of lipid molecules align hydrophilic heads in each sheet face the water while the tails face towards 1 quot 3 2 1 the interior and interact with each other Micelle 39 i tend to form from phospholipids that contain two hydrocarbon tails Liposomc Form spontaneously I l l lllllllllllllllllll llllllllllllllllllil I Phospholipid bilayer I Artificial Membranes as an experimental system When phospholipids are put in a an aqueous solution and agitated they form small vesicles called liposomes Planar bilayers were also constructed bilayer constructed across a hole in a cup separated by two solutions Used these to test for permeability across the membrane Selective Permeability of Lipid bilayers Lipid bilayers are highly selective Small nonpolar molecules move along the membrane much faster than larger molecules and charged substances 0 SMALL CO wouomomc MOLECULES benzene H70 glycerol How does lipid structure affect membrane permeability ethanol Amphipathic mature of phospholipids allows them to form membranes spontaneously However not all phospholipid bilayers are created equal amino acids 39 39 glucose nucleotides H Na HCO3K Caquot cr Mgquot Bond Saturation and Hydrocarbon Chain Length Affect Membrane Fluidity and Permeability When unsaturated hydrocarbon tails are packed into a bilayer kinks created by the carbon double bonds weaken the strength of the interactions that hold the tails together weakening the barrier to solutes sy g ilstic Packed saturated hydrocarbon tails have fewer spaces and stronger interactions As the length of bilayer the tail grows longer the forces that hold them together also become stronger making the 1W 3 mm WWW2 39 2 quot 5W39 membranes even denser Cholesterol reduces permeability of the membrane bulky steroid rings fill gaps in the hydrophobic section of bilayer Factors That Affect The Fluidity Of The Membrane 39 Latent movement Pup op 107 time per second once per month 3 Movement of phospholipids lquot on 1 m If 1 14 is Satanic J A39 39Jquotx39i39I1 i elils Unsaturated hydrocarbon tulle with kink b Membrane uidlly IV I quot gd 39 quot 39 3 39 39 39 I H u 39 l at ll l 39 u39 36 quotCelllierwbru39Fizleazweas I I 4 t 39v I t39tt VI liyi T L Jv 5 IJJ b b h e th ulj U b o dld 5 u b lu hlu h Cholesterol 0 Cholesterol within the animal cell membrane V 7 WWM 7 y ww er J Module 1 Page 22 How does temperature affect the fluidity and permeability of membranes Permeability is closely related to fluidity Most phospholipids are liquid at room temperature the phospholipids in the membrane have a consistency similar to olive oil As temperature drops the molecules in the bilayer move more slowly reducing fluidity and the hydrophobic tails pack even tighter At lower temperatures the lipid bilayers can even solidify 0 Low temperatures make usually permeable molecules impervious to the membrane Module 1 Page 23 63 How Molecules Move across Lipid Bilayers Diffusion and Osmosis Tuesday September 16 ZOM 159 PM Small uncharged molecules and hydrophobic compounds can cross membranes readily and spontaneously How is this possible Diffusion Solutes move randomly in all directions but when a concentration gradient exists there is a net movement from regions of high concentration to regions of low concentration Diffusion down a concentration gradient or away from higher concentration is a spontaneous process because it results in the increase of entropy Osmosis The movement of water is a special case of diffusion Osmosis only occurs when solutions are separated by a membrane that permits water to cross but holds back some or all of the solutesthat is a selectively permeably membrane 0 Only unbound water molecules are able to diffuse across the membrane 0 Flow from solution with low solute concentration into solution with high solute concentration Module 1 Page 24 64 Membrane Proteins Tuesday September 16 2014 336 PM CUL IullN quotICILG39MI PII Culwlun 39l 39Utlmlul6quothtlw wh Ill 39t Fluld Mosalc Model Amphipathic Proteins can be inserted into the bilayer Nonpolar residues in the middle ofthe primary structure could reside in the bilayer while polarcharged amino acids can be stable alongside the polar lipid heads and surrounding water E macelll la39 quotUid Carbohydrate Because secondary and tertiary structure are almost limitless in variety it is possible for proteins to form opening and thus a I 1 I function as channels cross the bilayer I I i quot 39 55 39 Development of the FluidMosaic Model Proteins that span the membrane integraltransmembrane proteins Proteins that bind to the membrane without passing through it peripheral membrane proteins Systems for Studying Membrane Proteins In order to test the hypothesis of whether or not proteins affect membrane permeability researchers needed a way to isolate and purify membrane proteins Detergents are small amphipathic molecules Once placed in a solution the hydrophobic tails interact with the hydrophobic tails of phospholipids and with the hydrophobic portions of transmembrane proteins These interactions displace the membrane phospholipids and end up forming watersoluble detergentprotein complexes that can be isolated Transported molecule 0 Channel plotein Thee broad classes or proteins that affect membrane permeability channels carriers and pumps Channels Allows ions and small molecules to pass thorough Passive transport is powered by diffusion along an electro chemical gradient i i O Electrochemical Carrier Proteins Also use faCIIItated dIfoSIon to allow larger molecules through mm quotmm 39 J quotquotquot MW Passive transport f Primary actiw transport int 9 direction 0 against the dilution Pumps Perform activeuses ATP to move objects against the chemical gradient electromem39cai gradient of electmhemical gradicm Cargo PassiveActive DownAgainst transport Gradient Channels Ionssmall PassiveSimple Down mOIECUIeS Secondary Active Transport 02 AKA Cotransport Carrier Larger Facilitated Down Uses electrochemical gradient set up by a pump to allow objects to move along a gradient Proteins molecules Glucose Pumps Ion against Active uses Down gradient ATP Sodium Potassium Pump 30 of ATP is used on NaquotK ATPase pumps Creates electrochemical gradient Net Movement 3 Na out of cell 2 K into cell f u X l I qan I A P0 t t i l39u Junonwa 4 NA39 hum MI39 Module 1 Page 25
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