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Chapter 2 Book notes, Biochem

by: Cassidy Zirko

Chapter 2 Book notes, Biochem BCH 110

Marketplace > University of Montana > Biology > BCH 110 > Chapter 2 Book notes Biochem
Cassidy Zirko

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Covers Hydrogens bonds, pH, Acids and Bases
Intro Biology for Biochemist
Scott Samuels
Class Notes
Biology, biochemistry
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This 4 page Class Notes was uploaded by Cassidy Zirko on Saturday February 13, 2016. The Class Notes belongs to BCH 110 at University of Montana taught by Scott Samuels in Spring 2016. Since its upload, it has received 44 views. For similar materials see Intro Biology for Biochemist in Biology at University of Montana.


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Date Created: 02/13/16
Biochemistry 110  Chapter 2: Water: The Solvent for Biochemical Reactions Week 2 2.1 Water and Polarity   Principal component of most cells   Electronegativity­ tendency of an atom to attract electrons to itself in a chemical bond   Oxygen and nitrogen are both highly electronegative   What is Polarity?  o Atoms with same electronegativity form a bond  electrons shared equally  between two atoms  o Differing electronegativity causes electrons to be shared unequally with one atom  having more of a negative charge  o Polar bonds­ difference in electronegativity between oxygen and hydrogen gives  rise to a partial positive and negative charge  o Nonpolar bond­ sharing of electrons in the bond is very nearly equal  o Having polar bonds doesn’t make it a polar molecule  o Dipoles­ bonds with positive and negative ends   Solvent Properties of Water  o Why do some chemicals dissolve in water while others do not?  Polarity of water determines  solvent properties   Ion­dipole and dipole­dipole interactions are responsible for attractions  between water molecules   Hydrocarbons are nonpolar   Interactions between nonpolar molecules and water are very weak   Some electrostatic attraction possible between induced dipole in water  molecules   Hydrophobic­ don’t like water   Hydrophilic­ water loving   Hydrophobic interactions­ interactions between nonpolar molecules  o Why do oil and water mixed together separate into layers?  Amphipathic­ having both polar and nonpolar portions   Interactions between nonpolar molecules are very weak­ depend on short  lived temporary dipoles   Temporary dipole can induce another dipole in a neighboring molecule,  similar to a permanent dipole   Van der waals interaction­ low interaction energy because of short lived  association with a dipole  2.2 Hydrogen Bonds   Hydrogen bonding­ electrostatic origin and can be considered a special case of dipole­ dipole interaction  Biochemistry 110   Partial positive charge when bonded with oxygen or nitrogen because of polar bond   Partial positive charge interacts with unshared pairs of electrons   Group with electronegative atom that is covalently bonded to hydrogen­ hydrogen bond  donor   Hydrogen bond acceptor­ electronegative atom that contributes the unshared pair of  electrons to the interaction   Why does water have such interesting and unique properties?  o Each water has 4 hydrogen bonds­ with donor and acceptor having 2  o In liquid water, hydrogen bonds are constantly breaking and forming new ones  o Hydrogen bonds weaker than covalent bonds  o Melting point and boiling point of water are higher than predicted  o Energy of attraction must be over come to melt ice or boil water  o Ice has lower density than liquid water  o Polar solute acting as donor or acceptor of hydrogen bonds when dissolved in  water   Other Biologically important Hydrogen Bonds  o Have vital involvement in stabilizing 3D structures  o Hydrogen bonding in proteins creates alpha helix and beta pleated sheets  2.3 Acids, Bases and pH  What are acids and bases? o Acid­ molecule that acts as a proton donor  o Base­ molecule that acts as a proton acceptor  o Degree of dissociation ranges from complete dissociation to very little  o Acid strength­ amount of hydrogen ion released when a given amount of acid is  dissolved in water A−¿ ¿ o Acid dissociation constant, K   H ¿     a [ ] K a¿ o Each acid has a constant that is fixed, greater constant, stronger acid  o No naked protons in a solution, (free hydrogen ions)   What is pH? o K ,wion product constant for water­ concentration of water has been added to  value, 55.5  o Wide range of possible hydrogen ion and hydroxide ion concentrations in aqueous solution   + o pH=­log[H ]  o pH values of some aqueous samples can be determined by that calculation  o pH of 7 is neutral, acidic is less than 7, basic is greater than 7   Why do we want to know the pH? Biochemistry 110  o It can be important to control the pH of a solution for optimum reaction  conditions  o Bad things can happen when there is pH fluctuations in the body  o Henderson­ Hasselbalch equation­ the relationship between pH and pK : a A−¿ ¿ ¿ ¿ pH=pKa+log¿ o Equation contains equal concentrations of weak acid and its conjugate base, pH of that solution equals the pKa value of the weak acid 2.4 Titration Curves   Titration­ experiment in which measured amounts of base are added to a measured  amount of acid   Equivalence point­ point in titration at which the acid is exactly neutralized   Near the inflection point, pH changes very little when more base is added   Monoprotic, diprotic­ number of hydrogens released   When pH of a solution is less than pK aof an acid, pronated form predominates, pH is  greater then deprontonated forms predominates  2.5 Buffers   Buffer­ something that resists change   Buffer solution­ resists change in pH when small to moderate amounts of a strong acid or  strong base are added   How do Buffers work?  o Increase in hydroxide ions shows that hydrogen ion concentration has decreased  and that pH increases  o Many reactions wont take place unless pH remains within some limits  o Buffers are very important in laboratory conditions   How do we choose a buffer? o pH of a sample being titrated changes very little around inflection point  o half of acid originally presented has ben converted to conjugate base   o pH at inflection point is based on pK  a o buffer solution can maintain pH at a relatively constant value because of presence  of appreciable amounts of both the acid and conjugate base  o buffer solution with low concentrations of both acid and base forms have low  buffering capacity   How do we make buffers in laboratory? o Use Henderson­ Hasselbalch to calculated actual values  o All that is needed are the two forms of the buffer present in the solution  o Making it starts with conjugate acid and added NaOH until have correct pH  Biochemistry 110  o Based on relationship between pH and pK  a base might be easier to use   Are naturally occurring pH buffers present in living organisms? o Buffer systems in living organisms are based on many types of compounds  o In living organisms, pH must stay very close to 7  o Carbon dioxide can dissolve in water to form carbonic acid which then  precipitates  o pH of blood and pressure of carbon dioxide in lungs is extremely important  o zwitterions­ compounds that have both a positive charge and a negative charge  o considered less likely to interfere with biochemical reactions that earlier buffers  o


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