Unit 2:Chemistry of Life

Unit 2:Chemistry of Life Atoms, Ions and MoleculesProperties of WaterAcids and BasesOrganic MoleculesChemical ReactionsEnzymes1Atoms, Ions and MoleculesThis topic looks at some Chemistry basics that are essential for understanding life. It defines and explains the roles of atoms, ions and molecules.2Atoms, Ions and Moleculeselement - substance that cannot be broken down chemically into any other substances

atom - matter that cannot be subdivided any further without losing its essential properties

3Subatomic particles Particles smaller than an atom1940: protons, neutrons, electrons, neutrinos, positronsProtons, neutrons, electrons building blocks from which atoms are madeprotons and neutrons in nuclei electrons in orbit around nucleiNeutrinos and positrons were somewhat peculiar particles discovered outside Earth's atmosphere and of uncertain origin or significance.4

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6CHONPS + 4Be sure to mention Mendeleev6

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9Atoms, Ions and MoleculesMolecule: 2 or moreatomsjoin together chemicallyCompound: molecule that contains 2 or more differentelementsAll compounds are molecules but not all molecules are compounds.10Chemical BONDSCovalentIonicPolar CovalentHydrogen11

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13Polar Covalent Bondselectrons shared by the atoms spend a greater amount of time, on average, closer to one nucleus than the otherdue to geometry of molecule and electronegativity differences result is a charge separation in the molecule, where one part of the molecule has a partial negative charge and one part has a partial positive charge14Polar Covalent Bondsmolecule is not an ion (no excess of protons or electrons)water is the most common but not the only molecule that can have polar covalent bondsother molecules that have polar covalent bonds are peptide bonds and aminesthe biological consequence of polar covalent bonds is that these kinds of bonds can lead to the formation of a weak bond called a hydrogen bond15Polar Covalent Bonds16

Hydrogen Bondsformed when a charged part of a molecule having polar covalent bonds forms an electrostatic interaction with a substance of opposite chargemolecules that have nonpolar covalent bonds do not form hydrogen bondsclassified as weak bonds because they are easily and rapidly formed and broken under normal biological conditionsunder the right environmental conditions, any compound that has polar covalent bonds can form hydrogen bonds17Hydrogen Bondsimportant in biological systemsexplains many of the properties of waterused to stabilize and determine the structure of large macromolecules like proteins and nucleic acidsinvolved in the mechanism of enzyme catalysis 18

19What characteristic of an atom gives it its chemical properties?the number of protonsthe number of neutronsthe number of electronsthe number of electrons in its outer orbital20

All life on earth depends on water; organisms are made up mostly from water and require it more than any other molecule. Hydrogen bonding among water molecules gives water several important properties that contribute to its important role in the biology of all organisms.

21States of Matter22

Cohesion & AdhesionCohesion water is attracted to other water molecules Adhesion water is attracted to other materials

oxygen end of water has a negative charge hydrogen end has a positive chargehydrogens of one water molecule are attracted to oxygen of another water molecule this attractive force is what gives water its cohesive and adhesive properties23Surface Tensioncohesion of water molecules at the surface of a body of waterall the water molecules on the surface of a quantity of water (a bead, cup, pond, etc.) are 'holding' each other together, creating surface tension24Cohesion & AdhesionSurface tension allows water striders to 'skate' across the top of a pond. Many objects are heavier than water, but because of surface tension, the water is able to hold up the metal.Surface tension is not the force that keeps boats floating. 25

2626Figure 2-13 Walking on water! Hydrogen bonds make this possible for some animals.Capillary Attractionrelated to adhesive properties of waterclick here for demonstrationwater 'climbs' up the straw as the water molecules are attracted to the straw moleculeswhen one water molecule moves closer to the straw molecules the other water molecules (which are cohesively attracted to that water molecule) also move up into the straw. 27

2828Walking across a sandy beach on a hot day, you can feel how easily sand heats up. By comparison, stepping into the cooler ocean that same day reveals that water resists warming. It takes a lot of energy to change the temperature of water even a small amount. Why? Again, we must look to hydrogen bonding for our answer.

The temperature of a substance is a measure of how quickly all of the molecules are moving. The molecules move more quickly when energy is added in the form of heat. When we heat water, the added energy doesnt immediately increase the movement of the individual water molecules. Rather, it disrupts some of the hydrogen bonds between the molecules (Figure 2-15 Water as a moderator of temperature change). As quickly as they can be disrupted, though, they form again somewhere else. And since the water molecules themselves dont increase their movement, the temperature doesnt increase. The net effect is that even if you release a lot of energy into water, the temperature doesnt change much. Because so much of your body is water, you are able to maintain relatively constant body temperatures.

2929Ice floats. This is unusual since most substances become more dense when frozen; as the molecules slow down, they pack together more and more efficientlyand densely. Consequently, they sink. Water, however, becomes less dense and as you might expect by now, this is due to hydrogen bonding. As the temperature drops and water molecules slow down, rather than becoming more and more tightly packed, they become less so. Each V-shaped water molecule bonds with four partners, via hydrogen bonds, forming a crystalline lattice in which the molecules are held slightly farther apart, causing ice to be less dense than water (Figure 2-16 Ice floats).

3030If you put a bit of table salt into a glass of water, it will quickly dissolve. This means that the charged sodium (Na+) and the chloride (Cl) ions that were ionically bonded together all become separated from each other. The sodium and chloride ions were initially attracted to each other because they are polar molecules, each carrying a slight charge. Water is able to pry them apart because, as a polar molecule, it too carries charges. The positively charged sodium ions are attracted to the negatively charged side of the water molecule, and the negatively charged chloride ions are attracted to the positively charged side (Figure 2-17 Solutions). Many substances are polar like water. That is why, like salt, they easily dissolve into it.

Non-polar molecules (such as oil) have neither positively charged regions nor negatively charged regions. Consequently, the polar water molecules are not attracted to them. Instead, when oil is poured into a container of water, the water molecules distance themselves from the oil, leaving the oil molecules in isolated aggregations that never dissolve. Why dont oceans freeze as easily as fresh water lakes?CohesionHeat capacityIce floatsWater is a good solvent31Fish live in water. What property of water is important for the survival of fish during the winter?CohesionHeat capacityIce floatsWater is a good solvent32Summary Properties of WaterCohesionAdhesionSurface tensionCapillary AttractionHigh heat capacityLow density as a solid33Acids & BasesAcid: substance that increases the hydrogen ion (H+) concentration in a solution Base: substance that removes hydrogen ions from a solution, resulting in an increase in the hydroxide ion (OH-) concentration.

34AcidH+ very reactiveExample: H+ can bind with atoms in metals, causing them to corrodeAcids can donate H+ to other chemicalsStomach acidhelps to kill most bacteria that you ingestenhances breakdown of chemicals in food enhances efficiency of digestion and absorption 35BasesLow H+; High OHBaking soda, Alka-seltzer, milk of magnesiaAntacidsOH ions bind with excess H+ ions, neutralizing the acidHousehold cleaners

36Acids & BasesAcidity of a liquid is measured as its concentration of hydrogen ionspH scale expresses this concentration in logarithmic units very acidic = pH 0neutral value = pH 7very alkaline (basic) = pH 14

37pH scale38

Organic CompoundsSubstances that contain carbon Carbon occurs in almost every chemical compound found in living thingsFour main types of organic compounds in living things: carbohydratesproteinslipids nucleic acids39Organic CompoundsCombination of carbon and almost any other elementUnique atomic structure allows a carbon atom to link up with as many as four other atoms of another Also links up with other carbon atoms to form long, stable chains, variety of combinations carbon can form with other elements is almost limitlessFYIscientists have already identified more than ten million organic compounds.

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