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BIOL 112 Lecture Notes Part 1.doc

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Biology (Sci)
BIOL 112
Joseph Dent

BIOL 112Winter 2011Lecture Notes Part ISmall moleculesThe below is mostly review of basic chemistryAtomic structure protons neutrons electrons24Mass of protonstandard unit of measure called the dalton OR amu 1 amu is roughly 17 x 10 gMatter anything that occupies space and has mass which is a quantity of matter circular definitions ftwInertia resistance to change of state of motionClassification of matterSeparable by physical meansmixtureHomogeneous uniform throughout eg salt solution or heterogeneous not eg milkfat in a waterbased mediumNot separable by physical meanssubstanceCompound decomposable by chemical process or element notAtomic massmass of neutrons protons and electrons in amu atomic mass unitsNeutrons and protons have mass 1 electrons have a mass of something like 00005Note that atomic mass is different from atomic weightatomic weight is the weighted average of the atomic mass of the isotopes of an elementRelative atomic mass is a synonym for atomic weight and this is rarely a whole numberAlso note that neutrons and protons dont have exactly the same mass we approximateFurthermore due to binding energy But in any case the lesson here is that atomic mass and weight are rarely whole numbers for several reasonsThe explanation in the lecture itself is a bit misleading and doesnt really account for the difference between atomic mass and weightThe periodic table classifies elements in groups and families primarilyIsotopes different number of neutrons but identical chemical properties determined by protons and neutronsHowever due to the number of neutrons can be unstable ie radioactiveemit alpha beta or gamma radiation from the nucleusChemical bonding Aufbau principle electrons fill up s orbitals before p orbitalsAtoms can form bonds until their outermost shell is filledCovalent bondssharing of electrons to some degree strong predictable lengths and angles can be double or TRIPLEPolar covalent bondswhen electrons are more attracted to one nucleus than the other eg with waterThis results in a dipoleOn the other hand in a CC bond for instance the electrons are shared quite equallyIonic bondsattraction of opposite charges basically covalent but electronegativity difference is greater usually 18not in scope of courseYoull learn if you havent already that a lot of explanations in basic chembio courses are simplifications ie liesvan der Waals forces interactions of electrons of nonpolar substancesHydrophobic interactions nonpolar substances in the presence of polar substancesBond energy energy needed to separate two bonded atoms under physiological conditions Electronegativity tendency of an atom to attract electrons when it occurs as part of a compoundIncreases as atomic radius decreases and nuclear charge increases ionization energy is similar but slightly differentLarge moleculesAcids and basesAcids donate hydronium ions H simplified as hydronium ionsStrong acids vs weak acidsstrongrelease many H ions simplified as they release all their ions weakonly someDepends on pKa value like covalentionic bonding there is a continuum but just pretend that what is said in this class is trueBases accept H release OHEx NaOH is a strong baseAmino group NH important part of many biological compounds principal component of protein 2weak baseWater weak base AND acid pH of pure water is 7 but almost all water is acidic due to dissolved ions gases eg CO etc27pH is concentration of hydrogen measured in logarithmspH of 710 molL
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