Foundations of Biology 1
Foundations of Biology 1
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Date Created: 08/24/14
Basic Chemistry of Life 82813 Part One Chemistry Learning Goal Look at slide of lecture 2 Cation positively charged Anion negatively charged Ionic bonds Opposites attract Ionic bonds are very strong bonds but however dissociate back into ions in water soluble Electronegativity how quotattached an element is to its outer electrons Cation electronegativity tends to be very low if non existent while anion electronegativity tends to be very high Electronegativity Scale Oxygen O gt Nitrogen N gt Carbon C Approximately Hydrogen H Covalent bonds electron sharing A Nonpolar covalent bond in hydrogen molecule 0 Electrons are shown to be superimposed on the bond to indicate that they are halfway between the two atoms shared equally B Polar covalent bonds in water molecule 0 Electrons are not shared equally O is more electronegative than H so partial charges exist on the O and H atoms Examples of Polar covalent bonds OH O is more electronegative OC Same as above NH N is more electronegative See Lecture powerpoint for examples of nonpolar covalent bonds Connections All biological interactions happen in the context of water solutions Water loves polar bonds Water interact with ionic polar and nonpolar compounds differently This has consequences for the behavior of all biological molecules as we will learn Why do I care about whether a bond is polar or nonpolar Nonpolar bonds don t interact with water but they can interact with each other o Fats and oils are hydrocarbons o The cell membrane is mostly nonpolar Nonpolar bonds tend to contain more chemical energy Polar bonds give water unique properties o Ice density evaporative cooling adhesion Polar bonds interact with water ions and other polar bonds o More polar bonds more soluble Basic Chemistry of Life 82813 o More polar bonds less likely to cross a cell membrane unaided Bonds are more likely to be polar when the two molecules are very far away in terms of electronegativity Hydrocarbons molecule with H and C only are held together by nonpolar covalent bonds The importance of Carbon o Focus Carbon can form up to four covalent bonds 0 Learning Goal Students should be able to explain how the chemical properties of carbon allow the formation of endless diverse molecular structures and be very familiar with common repeated motifs of organic molecules rings functional groups and their properties Carbon forms the skeleton of all organic compounds o Carbon can form lines rings and other intricate shapes o Single and double bonds alter the shape Functional groups gives organic molecules their unique properties o Look at Powerpoint for diagrams of functional groups o Memorize these Part two water and hydrogen bonds 0 Learning goal Students should understand how the properties of water affect the three dimensional structures and stabilities of macromolecules macromolecular assemblies and lipid membranes o Focus is on water39s polarity behavior hydrogen bonding and effect on solutes Water is polar When water molecules are near each other partial positives of Hydrogen molecules attract between separate molecules while the partial negatives of Oxygen molecules also attract o Hydrogen bonds Water interacts with itself like crazy Ice is formed when water molecules form hydrogen bonds with one another Ionic compounds interact with dissolve in water o They form hydrogen bonds with water o They dissociate into component ions Polar compounds interact with dissolve in water o Polar regions form hydrogen bonds with water o Hydrophilic Covalent bonds do not come apart in pure water o They can dissolve but they generally do not dissociate Nonpolar compounds do not interact with water o They cannot form hydrogen bonds with water o Hydrophobic Basic Chemistry of Life 82813 Hydrogen bonding sometimes pull Hydrogen atoms away pH scale measures the amount of Hydronium ion in liquids Water has a polar structure so it can therefore form hydrogen bonds Water molecules interact with each other specific heat adhesion cohesion evaporation pH Forming hydrogen bonds between molecules Water molecules cannot interact with nonpolar molecules o Hydrophobic molecules do not interact form layers or bubbles Water molecules interact with polar or charged solutes o Hydrophilic molecules o Ions dissociate in water directly due to hydrogen bonding o Polar compounds interact and can dissolve Hydrogen bonding holds molecules together into 3d Structures General rule Anything that alters or disrupts hydrogen bonding will adversely affect cells o Temperature Excessive ions in solution alterations in pH When we want to separate two strands of DNA we heat them The two strands come apart from each other What might be holding the strands together o Both Ionic bonds and Hydrogen bonds would be disrupted by heat while Covalent bonds would not We want to separate two strands of DNA we heat them But the two strands remain intact What kind of bonds are strong enough to keep the molecules together o Covalent bonds because ionic bonds and hydrogen bonds would be disrupted by heat Lipids consist primarily of CH bonds Are they primarily hydrophobic or hydrophilic o Hydrophobic because no polar bond exists within the molecule Lipids consist primarily of CH bonds How do they react in water o They float or sink but do not dissolve Learning goal Students should be able to explain the step wise progression that resulted in the first cell and how the principles of natural selection apply to selfreplicating compounds o Focus I How life can assemble and complexity can arise without breaking laws of thermodynamics I Selfreplicating molecules and Natural Selection Does life follow the laws of physics 0 YES Chemical Reactions follow rules o Reactants interact to form products o All reactions are reversible one direction is spontaneous the other requires extra energy In any reaction some energy becomes unusable Building complex macromolecules always requires extra energy The universe is tending towards disorder or Entropy o For every action there is some energy lost Evolutionary Theory Descent through modification o All life is ce based o All life comes from life OOO Basic Chemistry of Life 82813 o Natural Selection is the mechanism that drives adaptive evolution o All life on Earth can be traced back to singe ceed life But where did the first cells come form o Dat Primordial Oooozzeee Abiogenesis Life from nonlife Stepwise building of complex molecules from less complex molecules o Simple molecules like CO CN CO2 H NH H20 and N2 I Energy inputs light heat radiation I Simple organic compounds like HCN H2CO 0 Energy inputs light heat radiation electrical discharges 0 Complex organic compounds Amino acids sugars nitrogenous bases UreyMiller experiments Evidence that complex organic molecules can under the right conditions selfassemble from simpler molecules Complex Organic Compounds o Polymerization into longer macromolecules o Early proteins sugars nucleic acids lipids Early sugars Were ALL the building blocks there o Yes Formaldehyde will result in 5 6 and 7 carbon sugars In addition they found simple sugars on a meteorite Can we make them polymerize under abiotic conditions 0 No Early proteins o Yes In fact reexamination of Miller39s vials found all of the 20 amino acids and more Can we make them polymerize under abiotic conditions o Yes RNA and DNA Maybe First mystery the 5carbon sugars of nucleic acids ribose These form easily enough but we don t know why the 5carbon sugars predominated Second mystery the pyrimidines C U and T The nitrogenous bases A and G form easily from HCN reactions but we have yet to discover a way to create C U and T under eary Earth conditions Can we make them polymerize under abiotic conditions o Yes OOOOO
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