BIO 181 Notes
BIO 181 Notes BIO 181
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This 20 page Class Notes was uploaded by Ernie on Monday February 15, 2016. The Class Notes belongs to BIO 181 at Arizona State University taught by Chakravadhanula, Farrokh, Konikoff in Winter2015. Since its upload, it has received 50 views. For similar materials see General Biology 1 in Biochemistry at Arizona State University.
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Date Created: 02/15/16
Cellular Respiration Notes The last bond on ATP is very high energy, and when this breaks off this energy is used Condensation reaction- Reattach the Phosphate to ADP to make it ATP again Glucose can be broken to produce ATP 1) Glycolysis- Make glucose into Pyruvate which produces 2 ATP molecules After this 2 Pyruvates are converted into Acetyl CoA, these will go through the Kreb Cycle 2) Kreb Cycle- Acetyl CoA goes through and NADH and FADH2 are produced along with CO2 NADH and FADH2 assist the mitochondria in creating a proton gradient, inside inner membrane of mitochondria, this will help with ATP Synthase, this takes an ADP and Phosphate group and combines them to create ATP 3) Electron Transport Chain Cellular Respiration Equation— C6 H12 O6 (1 Glucose) + 602 (Six Oxygen) 6CO2 (Six CO2) + 6H20 (6 Water) + Energy/ATP Bio Notes 18.1 An Overview of Gene Regulation and Information Flow Flow of information from DNA to activation is represented as DNA mRNAProteinActivated protein DNA to mRNA represents Transcription, which is the creation of messenger RNA/mRNA mRNA to Protein represents Translation which is when ribosomes read the information on the mRNA and use this to synthesize proteins Protein to activated protein represents modifications to the protein that can change shape and activity Ways to Avoid Producing Unnecessary Proteins 1. Transcriptional Control- when regulatory proteins affect RNA polymerase’s ability to bind to a promoter and start transcription, Transcription is prevented 2. Translation Control- Prevent the mRNA from being translated into protein, occurs when regulatory molecules alter the length of mRNA’s life or affect the first two phases of translation, Initiation/Elongation 3. Post-Translation Control- Regulating the activation of proteins *All of these occur in bacteria Transciption-Control is the most efficient since it stops at the earliest possible stage Translation-Control- allows cell to make rapid changes in the amounts of different proteins, because mRNA is already present and available to be translated Post-Translation Control- Gives the most rapid response because only one step is needed to activate a protein All have trade offs with speed and efficiency Transciption Control is slow but energy efficient Post Translation Control is fast but very costly as far as energy goes Gene expression is not ALL OR NOTHING, there can be varying levels of expression for genes The E. Coli bacteria’s main food supply is glucose it will eat lactose but only if all glucose is gone To eat lactose the E. Coli first transports the sugar into its cell, and then has an enzyme break down the cell into glucose that can be used Inducer- A small molecules that will trigger the transcription of a certain gene This makes the gene more prominent if induced 18.3 Negative Control of Transcription Transcription is regulated in 2 ways in principle 1) Negative Control- When a “Repressor protein” binds to DNA and stops the process of transcription 2) Positive Control- When a “Activator protein” binds to DNA and causes transcription Negative Control- Brakes on a car Positive Control- Gas Pedal on a car Lactose- Unbinds the negative control so it “releases the parking brakes” Operon- Set of coordinately regulated bacterial genes that are transcribed into one mRNA lac operon- Genes involved with lactose metabolism 3 Hypotheses in Model of lac operon Regulation 1. lacZ, lacY, & lacA genes are adjacent and are all transcribed into a single mRNA initiated from the single promoter of the lac operon AKA Cotranscription- Causes coordinated expression of the three genes 2. The repressor is encoded by lacI which binds to DNA and prevents transcription of lac operon genes (lacZ, lacY, & lacA) lacI is constantly expressed and repressor binds to a section of DNA in the lac operon called the “Operator” 3. The Inducer/Lactose binds to a repressor, this makes the repressor change shape, due to the change in shape the repressor falls off of the DNA it is binded to AKA Allosteric Regulation- small molecule binds to a protein and causes the protein to change shape and activity, allows transcription to continue Glucose has been seen to prevent expression of lac operon Induce Exclusion- Glucose preventing the transport of an inducer Gene Expression- Regulated by physical contact between regulator proteins and specific regulator sites in DNA Repressor Proteins are always produced, they’re activity is just altered when they are needed to be used to represses 18.3 Negative Control of Transcription Transcription can be regulated in two ways 1) Negative Control- When the regulatory protein known as a Suppressor binds to the DNA and shuts down transcription 2) Positive Control- Regulatory Proteins known as an Activator binds to DNA and triggers transcription Negative Control= Car Brakes Positive Control= Acceleration/Gas Pedal Lactose releases the brake on the suppressor protein LacI Gene- Codes for a repressory protein that uses negative control on LacZ and LacY Bio Reading Notes 2-17-2016 9.1 An Overview of Cellular Respiration ATP has very high potential energy so it is not stable and not stored, cells contain enough ATP to last 30 seconds to a few minutes Most of the glucose used to make ATP comes from photosynthesis Glucose is not burned in cells it is oxidized in cells through many redox reactions Respiration fully oxidizes Glucose while Fermentation does not Respiration therefor releases more energy than Fermentation Chemical Energy in Glucose to Chemical Energy in ATP is a 4 Step Process 1) Glycolysis- One carbon of the glucose is broken into 2 molecules of the 3 carbon compound Pryuvate, ATP is produced from ADP and Nicotinamide Adenine Dinucleotide (NAD) is reduced to create NADH 2) Pyruvate Processing- Pyruvate is processed and releases one CO2 molecule, while the remain 2 carbons from the original 3 in Pyruvate are used to form acetyl CoA, oxidizing Pryuvate causes more NAD being reduced to NADH 3) Citric Acid Cycle- Acetyle CoA is oxidized into 2 molecules of CO2, while this is happening more ATP and NADH are created and Flavin Adenine Dinucleotide FAD reduces and forms NADS2 4) Electron Transport and Oxidative Phosphorylation- The electrons from NADH and FADH2 move through ETC/ Electron Transport Chain, the energy released in this chain of redox reactions is used to create a proton gradient across the membrane, this flow over the gradient is used to create ATP Cellular Respiration- Any suite of reactions that uses electrons harvested from high energy molecules to produce ATP with an electron transport chain All cells require Energy and Carbon They require a source of high energy electrons to generate chemical energy in the form of ATP They also require a source of Carbon containing molecules that can be used to synthesize DNA, RNA, Proteins, Fatty Acids, and other molecules Catabolic Reactions- Break down molecules, these often produce ATP Anabolic Reactions- synthesis larger molecules from smaller molecules, they use ATP Enzymes normally break down fats to releases glycerol and convert the fatty acids into Acetyl CoA Glycerol can be broken down further and enter glycolysis, while Acetyl CoA enters the Citric Acid cycle Proteins can be used to create ATP One molecule can have many different functions in the cell Catabolic and Anabolic pathways are intertwined By a cell regulating key reactions it can maintain homeostasis 9.2 Glycolysis: Processing Glucose to Pyruvate Metabolic processes can occur outside of an organism All 10 reactions of glycolysis occur in the cytosol in both Eukaryotes and Prokaryotes 1) Glycolysis starts by using ATP, it uses 2 ATP molecules before producing any 2) Each molecule of glucose produces 2 molecules of NADH and 2 of ATP and 2 Pyruvates 3) Phosphate group moves onto an ADP making it ATP Substrate Level Phosphorylation- Enzyme catalyzed reactions that produce ATP Energy to produce ATP comes from phosphorylated substrate not a proton gradient However ATP comes from proton gradient through oxidative phosphorylation Phosphofructokinase- Causes the synthesis of fructose In this ATP acts as a regulator Glycolysis 1) Starts with one 6 carbon glucose and ends with 2 3 carbon pyruvate molecules, the reaction happens in the cytoplasm and the energy that is released is used to produce 2 ATP and 2 NADH 9.3 Processing Pyruvate to Acetyl CoA Cristae- Sac like structures that fill the interior membrane, it is connected to the main part of the membrane by short tubes Mitochondrial Matrix- Inside the inner membrane, but outside the Cristae Pyruvate moves across mitochondrion’s outer membrane through pores CoA- Reacts with pyruvate, acts as a coenzyme by accepting and moving Acetyl group Pyruvate reacts with CoA and creates acetyl CoA Pyruvate Dehydrogenase- Enzyme complex where pyruvate reacts with CoA and creates Acetyl CoA In eukaryotes this is located in the mitochondrion matrix In Bacteria and Archaea this occurs in Cytosol While Pyruvate is being processed one of the carbons in Pyruvate is oxidized to CO2 and NAD is turned into NADH, the remaining carbon acetyl unit becomes CoA Pyruvate, NAD and CoA go in CO2 NADH and Acetyl CoA comes out If ATP is abundant the process will cease Large supplies of a product will slow down/stop the Pyruvate process while low supplies of the product and high supplies of the reactants will increase the process 9.4 The Citric Acid Cycle: Oxidizing Acetyl CoA and CO2 Carboxylic Acids- Redox reactions that oxidize small organic acids Energy is released by the oxidation of one molecule of Acetyl CoA is used to create 3 molecules of NADH and one of FADH2 and one of GTP/ATP ATP or GTP depends on the cell being created In eukaryotes the enzymes for the citric acid cycle are in the mitochondrial matrix Citric Acid Cycle has many regulations at many points Citric Acid Cycle- Begins with 2 Carbon Acetyl molecule in the form of Acetyl CoA and ends with the release of 2 CO2, the energy that is released by this is used to create 3 NADH 1 FADH2 and 1 ATP/GTP for every Acetyl oxidized 9.5 Electron Transport and Chemiosmosis: Building a Proton Gradient to Produce ATP Electron Transport Chain- Molecules responsible for oxidation of NADH and FADH2 As electrons are moved the energy released by the redox reactions is used to move protons across the inner membrane of mitochondria Ubiquinone- Moves quickly through hydrophobic interior of the inner of the mitochondrial membrane Cytochrome C- Acts as a shuttle that transfers electrons between complexes ATP Synthase- Enzyme to synthesis ATP ETC- Used to pump protons across inner membrane of mitochondria from the matrix to the intermembrane space, after the gradient is established an Enzyme/ ATP Synthase will synthesis ATP Chemiosmosis- Use of a proton gradient to drive energy requiring process like the production of ATP ATP production relies on a proton motive force ATP can be produced without a ETC but needs proton motive force ATP synthase can be done in reverse rebuilding a broken proton gradient Glucose can produce 29 ATP Species that need oxygen to accept electrons for respiration are called Aerobic Cells that do not require oxygen to accept electrons are anaerobic Aerobic is more successful in respiration 9.6 Fermentation Fermentation- Metabolic Process that regenerates NAD by oxidizing stockpiles of NADH, the electrons that are removed from NADH are moved to pyruvate or a molecule derided from pyruvate instead of an ETC Allows cells to grow without an ETC Lactic Acid Fermentation- Regenerates NAD by forming a product molecules called lactate a form of lactic acid Fermentation is very ineffective compared to Aerobic Cellular Respiration, due to Oxygens high electronegativity Usually used when Oxygen runs out to produce ATP Faculatitve Anerobes- Organisms that are able to switch between Cellular Respiraion and Fermnetation fdsfddfs What Happens to Energy in Chemical Reactions Free Energy- Amount of energy that is available to do work If Electrons are close to negative charges and far from positive charges it has a high potential energy Potential Energy- function of the ways its electrons are configured Enthalpy- Total amount of energy in a molecule When a reaction releases heat it has a Negative change in heat (because it is losing heat) and is also exothermic If a reaction brings in heat change in heat is positive and is called endothermic If the product of chemical reaction are less ordered than the reactants than entropy or change in S is increased S=Entropy=Disorder In order to determine if a reaction is spontaneous it is needed to assess the combine contribution of a change in heat and a change in disorder This is used with Gibbs free-energy change or change in G Change in free energy = Change in Enthalpy minus Temperature times the change in Entropy Exergonic- When change in G or free energy is less than zero When change in free energy is greater than 0 reactions are not spontaneous and are called Endergonic When change in Free energy is 0 reactions are at an equilibrium Spontaneous Reactions run in a direction with lower free energy in a system Exergonic- Spontaneous and release energy Endergonic- Nonspontaneous and need an input of energy to proceed The number of collisions between substances in a mixture depends on their temperature and concentration 1) Higher concentrations mean a higher likelihood of collisions and reactants will proceed quicker 2) When temperature is high than reactants move faster and collide more frequently Higher Concentration and Temperatures should speed up Chemical Reactions 8.2 Nonspontaneous Reactions May Be Driven Using Chemical Energy Endergonic Reactions- Require Energy Exergonic Reactions- Release Energy Energetic Coupling- Interaction between an Exergonic Reactions can supply energy needed for an Endergonic Reaction In Cells this happens with the transfer of either a 1) High energy electrons 2) Or a phosphate group Reduction-Oxidation Reactions/Redox Reactions- Reactions that involve the loss or gain of electrons If an atom loses an electron it is “oxidized” Oxidation- Losing Electrons Reduction- Gaining Electrons These are always paired together because one atom must gain an electron if another atom loses one In a Redox Reaction- An electron can move from one atom too another or it can just shift in a covalent bond between two atoms Electron Donor- One that gives an electron Electron Acceptor- One that receives an electron Molecules with a lot of C-H Bonds have a lot of potential energy Molecules that are oxidized have a lot of C-O bonds, these loss potential energy Reduction Reactions usually add H’s Oxidation Reactions usually remove H’s ATP is so usefully because it has a large amount of potential energy Phosphorylation- Addition of a phosphate group to a substrate When Reactant molecules in an endergonic reaction are phosphorylated the free energy released in phosphorylation is coupled to endergonic reaction to make the combined overall reaction exergonic 8.3 How Enzymes Work Enzymes- Are catalysts, they bring substrates together in a precise orientation that makes the chances of a reaction more likely Geometry and chemical properties determine what reactions certain enzymes will cause Before Reactions Occur 2 things must happen 1) Reactants need to collide in a precise orientation 2) Have enough kinetic energy to overcome repulsion between electrons that come into contact as a bond forms Enzyme Active Site- Where enzymes bring substrates molecules together in a substrate Support chances of the electrons interacting The active site is usually located in a cleft within the globular enzyme Enzymes are not static they are flexible and dynamic, many enzymes change when reactant molecules bind at the active site This is called an Induced Fit Transition State- When the interaction between the substrate and the enzyme is at maximum and unstable, when the “key is locked” Activation Energy- Required to strain chemical bonds in substrates so they can enter the Transition State Reactions Happen when Reactants have enough Kinetic Energy to reach the transition state, Kinetic Energy also depends on the temperature of the molecule The more unstable the transition state the higher the activation energy, and the less likely the reaction will proceed quickly Reactant Rates depend on the kinetic energy of reactants and the activation energy of the particular reaction/ the free energy of the transition state Interactions with amino acid R groups at enzyme active site stabilize the transition state and lower the amount of activation energy required for the reaction to continue An enzyme only changes the free energy of the transition state Enzyme Catalysis 3 Steps 1) Initiation- Enzymes orient reactants precisely as they bind at specific locations within the active site 2) Transition State Facilitation- In the active site reactants are more likely to reach transition state catalyzed reactions are much faster than those not catalyzed 3) Termination- Products have less affinity for active site than transition state does, the enzyme returns to the original form and the products are released When substrate concentration is low then speed of enzyme catalyzed reactions increases At intermediate substrate concentrations the increase in speed slows down At high substrate concentration reaction rate plateaus at a max speed 3 Enzyme Helpers 1) Cofactors- Inorganic Ions which reversibly interact with enzymes, thought to be involved with catalysis in early chemical evolution 2) Coenzymes- Organic molecules that reversibly interact with enzymes 3) Prosthetic Groups- Non-amino acid atoms/molecules that are permanently attached to proteins These are usually the part of the active site and play role in stabilizing transition state Reading Notes 2.2 Properties of Water and Early Oceans Life arose from water and continues to this day 75% of a typical cells volume is consisted of water Water is the most abundant molecule in organisms Solvent- An agent for dissolving substances and getting them into solution Water is a very good solvent which is what makes it so fundamental for life Substances are more likely to come together and interact when they are solutes or when they are in water The polarity of water helps it to be such a successful solute When water molecules interact the negatively charged Oxygen is attracted to the positively charged Hydrogens this creates weak Hydrogen Bonds Hydrophilic- A polar/charged molecule, since it has a charge it can interact with water Hydrophobic- Little to no interactions with water because the molecules are nonpolar/ have no charge Cohesion- The attraction between molecules that are similar, water is cohesive due to Hydrogen bonds that form between Water molecules Adhesion- Attraction between unlike molecules, usually seen as liquid and solid surfaces interacting Surface Tension- Water at the surface cannot interact with as much water as water inside a glass so there is a stronger connection between water molecules at the surface, this explains why it hurts to belly flop Water’s surface tension is extremely high due to the stronger Hydrogen bonds at the surface Water is denser than ice this is because the molecules are packed more densely than in ice If ice was not less dense it would not float on water Specific Heat- Amount of energy required to raise the temperature of 1 gram of a substance by 1 degree Celsius Water has a very high specific heat limit, because the energy must break the Hydrogen bonds before it can make the molecules move faster As a molecule increases in polarity the more amount of energy is needed to change its temperature Heat Vaporization- Energy required to make 1 gram of liquid a gas Water also has a very high Heat Vaporization limit Chemical Reaction- One substance combines with another or is broken down into a different substance Atoms are rearranged, chemical bonds are broken, and new bonds are created “Dissociation”- The chemical reaction that occurs between water molecules Acids- Substances that give up electrons and raise hydronium ion concentration of water Adding an acid increases proton concentration Bases- Substances that receive a proton in a chemical reaction and lower hydronium ion concentration Adding a base lowers proton concentration Water can act as an acid or a base Mole- 6.022x10^6 the mass of one mole of any substance is equal as its molecular weight in grams Molecule Weight- Sum of atomic weights of all the atoms in a molecule Molarity- Number of moles present in a substance per liter of solution pH- Indicates the concentration of protons in a given solution Water has a pH of 7 which is neutral Buffers- Compound that minimize the changes in pH, these help to maintain Homeostasis 2.3 Chemical Reactions, Energy, and Chemical Evolution Theory of Chemical Evolution- Simple molecules had chemical reactions over and over until complex organic molecules were created this could have occurred in 2 environments 1) The atmosphere- Dominated by gases 2) Deep-sea Hydrothermal vents- Extremely hot rocks on contact with sea floor, these have many gases along with minerals In Chemical Reactions the Reactant/Initial Molecules are on the left and Products/Resulting reactants are on the right When there are two arrows in a Chemical Reaction “equation” the reaction is reversible Chemical Equilibrium- Dynamic but stable state after chemical reaction Temperature can also effect chemical equilibrium Endothermic change- Heat is absorbed in the process Exothermic- Heat is released in process Energy- Capacity to do work or to supply heat this exists in two ways 1) Stored Potential 2) Active Motion Electrons will come to a shell closer to the Nucleus if possible, this is because an outer shell electron has more potential energy Chemical Energy- Potential energy that is stored in chemical bonds Kinetic Energy- Energy of motion Thermal Energy- Kinetic energy of a molecular motion Temperature- A measure of how much thermal energy the molecules posses Low Temperature- Molecules move slowly High Temperature- Molecules move quickly Heat- Transferred energy between two objects with different temperatures Energy- can only be transformed and transferred never created or destroyed Chemical Reactions are spontaneous if they can be caused on their own without external forces two factors determine if a reaction is spontaneous 1) When the Product molecules are less ordered than the reactant molecules *Entropy- Amount of disorder in an environment Entropy always increases in a isolated environment 2) If a product has lower potential energy than its reactants If the electrons in a product are held more tightly together than the reactants than it has a lower potential energy Heat- Increases Entropy in an environment Lecture Notes 2/17/2016 Energy Overview Clicker Questions 1. F 2. A 3. E 4. A 5. B 6. A 7. B/D/F 8. A 9. B Energy input is needed when making simple molecules into complex molecules Energy is released when complex molecules break down into simple molecules Laws of Thermodynamics 1) Energy is never created or destroyed 2) It takes energy to impose order on a system This is why we need energy to make complex molecules but don’t need energy to break down complex molecules Complex molecules are more ordered than simple molecules Where Does Energy Come From Cells Get Energy from 2 sources 1) Light 2) Chemicals More carbohydrates means that it will have more energy, calories are correlated with carbs Anabolic Reactions – Build complex from simple Catabolic Reactions- Break down complex into simple How is Energy Stored ATP is the most common molecule for energy storage Triphosphate is the important part for energy storage of ATP, if a phosphate is taken away energy will be released Change in free Energy that is positive means energy is inputted Delta G is Greater than 0 Change in Energy is negative then energy is released Delta G is less than 0 *Delta G is the Change in Energy ATP Hydrolysis is making ATP into ADP, which is removing a phosphate from ATP This takes the Triphosphate and makes it Diphosphate How Does ATP provide energy for reactions? Endergonic Reaction Alone Endergonic Reaction coupled to ATP breakdown If energy is needed for a reaction it is not spontaneous If energy is not needed the reaction is spontaneous
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