Chemical Principles for Biochemistry

Transcription

1 Although this is an introductory course in biochemistry, a certain background in chemistry is assumed. This section outlines certain principles and enumerates those terms and structures it is assumed that you know. You should read this section and assure yourself that you can define the terms and answer the questions posed. TABLE OF CONTENTS I. Definitions page 2 II. Principles page 3 III. Logarithms page 4 IV. Review of ph, Acids, Bases, Dissociation page 6 V. Functional Groups page 7

2 I. Definitions: It is assumed that you can define the following terms. If you cannot and if no definition is given you should refer to an elementary chemistry text to obtain one Atom: Atomic Weight: Atomic Number: Isotope: Molecule: Molecular Weight: Mole: Element: Compound: Gram Atomic Weight: Gram Molecular Weight: Molar: Milli: Gram: Liter: Group: Chemical Bond: Equivalent Weight: Normal Solution: Ion: Anion: Cation: Electron: Anode: Cathode: Degree Centigrade: Proton: Reactant: Product: Stoichiometry: The number 6.02 x It is the number of atoms in a gram atomic weight of an element. It is also the number of molecules in a gram molecular weight of a compound. The atomic weight taken in grams, it contains one mole of atoms. The molecular weight taken in grams, it contains one mole of molecules. A solution containing one gram molecular weight of a substance in one liter of solution. A prefix meaning one thousandth : a milliliter is 1/1000 of a liter: a millimole is. A collection of atoms that act as a functional whole: a hydroxyl group OH: a carboxyl group COOH. Sometimes referred to as a moiety. A solution that contains one equivalent weight of a compound per liter of solution is referred to as one normal or 1 N. The proportions of reactants in a chemical reaction. 2 P age

3 II. PRINCIPLES: The Law of Fixed Proportions: Chemical reactions involve whole numbers of atoms or molecules which combine or react in definite proportions as integral units. Thus 2H 2 + O 2 2H 2 O specifies the number and kinds of molecules that react to give a product which has a definite composition. In chemical reactions, atoms are neither created nor destroyed. The same number and kind of atoms are present in the product as were present in the reactants. Thus all reaction equations should balance; i.e. has the same number and kind of atoms on each side of the arrow or arrows. The Law of Mass Action: a.) Equilibrium Reactions Many reactions are reversible; that is, reactants can form products and products can form reactants. When such a reaction is initiated by mixing reactants together, products are formed rapidly at first and then more slowly as the concentration of reactants falls. As the products accumulate, however, the reverse action of products to give reactants increases in rate. A condition is reached in which both reactions are occurring at the same rate. This is the equilibrium condition. Equilibrium reactions are indicated by, irreversible reactions by. An example of an equilibrium reaction: b.) The Equilibrium Constant When temperature, pressure and other experimental variables are held constant, the ratio of products to reactants in an equilibrium reaction is constant. A + B C + D The constant ratio in this case is [C] [D] [A] [B] Where [ ] signifies concentration in moles/liter (molar, M) The constant is called the equilibrium constant, Keq. c.) The Law of Mass Action In a reaction that has reached an equilibrium condition, the addition of a reactant will drive the reaction "to the right" (to form more product) until the equilibrium condition is again achieved. Conversely, the removal of a reactant will pull the reaction "to the left" (to form more reactant) until equilibrium is reestablished. 3 P age

4 III. Logarithms A. Logarithms The logarithm of a number, N, to the base a (log a N), is the exponent of the power to which a must be raised in order to obtain N. That is, if a x = N then, x is the logarithm of N to the base a. We write: if a x = N, then x = log a N. Thus, 4 3 = 64, hence log 4 64 = = 100, hence log = = 67.6, hence log = 1.83 Logarithms to the base 10 are called common logarithms. The only other number that is used extensively as a base is the irrational number denoted by the letter e and is approximately Logarithms to this base are called natural logarithms. Thus, e = 388 or log e 388 = where e = (approximately). For simplicity, we adopt the following notation: log N (base omitted) will always mean log 10 N In N will mean natural logarithm of N or log e N Whenever any base other than 10 or e is used, the base will be inserted. You need to be familiar with how to handle elementary operations with common logarithms (log). B. Properties of Logarithms The logarithm of the product of two or more numbers is equal to the sum of the logarithms of the separate numbers. Thus, Property # 1: log 10 (MN) = log 10 M + log 10 N etc... Other commonly used properties: Property # 2: log 10 M = log 10 M log 10 N N Property # 3: log 10 N q = q log 10 N C. Characteristics and Mantissa In general, the common logarithm of a number consists of an integer (positive, negative, or zero) called the characteristic, and a decimal part called the mantissa. Since = 7.64, we may write: log = Using Property # 1 (above), we can determine the following: since 76.4 = 7.64 x 10 we have, log = log log and, since log = 1, this becomes log = log = = Similarly, we can apply Property # 2 (above), 4 P age

5 log = log = log log = = If the digits in a number are 764, then the mantissa is.883, and remains the same regardless of the position of the decimal point. Additionally, only the mantissa is obtained from logarithm tables, while the characteristic is supplied from the following rule: If the decimal point comes after the first figure (as in 7.64) the characteristic is zero and the logarithm is For each place the decimal is moved to the right from this standard position, add one (or if moved to the left, subtract one). So, to obtain the logarithm of 7640, the characteristic is 3 and the mantissa remains.883 (the log is 3.883), while for , the characteristic is 4 (the log is 3.117). D. Problems Check the following: 1) log 10 (10 7 ) = 7 2) log 10 (10 2 ) = 2 3) log 10 (10 24 ) = 24 4) log 10 (10 13 ) = 13 5) if log 10 N = 6, N = ) if log 10 N = 4, N = ) log 10 (78) = ) log 10 (520) = 2.72 E. Natural logarithms using the Mannheim Trig rule The relationship between the natural logarithm or, logarithm to the base e of N (ln N), and the common logarithm or, logarithm to the base 10 (log 10 N), is: ln N = ln 10 x log 10 N. The value of ln 10 is so this equation is ln N = log 10 N Therefore to find ln N, we find log 10 N and multiply it by P age

6 IV. Review of ph, Acids, Bases, Dissociation 1. A neutral solution is one where [H + ] = [OH ] = 10 7 M and ph = 7.0 (in simpler terms, at ph = 7, the [H + ] = 10 7 M). Additionally, [H + ] x [OH ] = These equations hold true for all aqueous solutions. 2. ph + poh =14. For a solution with a ph of 4.0, the poh will be 10. [OH ] will be M. 3. Acidic solutions have [H + ] > 10 7 M, and ph < 7.0; basic solutions have [H + ] < 10 7 M and a ph > An acid is any substance (compound, positive ion, or negative ion), which can dissociate to give a proton [H + ] to the solution; it is a proton donor. A base is any substance, compound, or ion, which can combine with a proton (or remove a proton from solution); it is a proton acceptor. 5. Every acid exists in solution in equilibrium with H + and a conjugate base the substance resulting from loss of H+ by the acid. Such acid base pairs are termed conjugate acid base pairs. In general: Acid Conjugate Base + H + Examples: The carboxylate ion is the conjugate base of the carboxylic acid. The amine is the conjugate base of the substituted ammonium ion. 6. The acidic dissociation constant (K a ) is the equilibrium constant for the interaction of an acid, its conjugate base, and H +. K a = [Conj. Base] [H + ] [Acid] Basic dissociation constants, K b, are rarely used since the realization that every base is in equilibrium with H + and its conjugate acid. It is more common to use the expression pk a rather than K a itself. Like ph and H + : pk a = log 10 1/ K a = log 10 K a Note the reciprocal relationship between K a and pk a ; as K a values increase, pk a values decrease. 7. Strong acids completely dissociate in solution (i.e. the equilibrium lies far to the right). Weak acids incompletely dissociate in solution; [Acid] is relatively high compared to [H + ] and [Conj. Base]. Acids found in organisms are usually relatively weak. 6 P age

7 Examples of strong acids include HCl, HNO 3, and H 2 SO 4 whereas strong bases include NaOH and KOH. In solution, strong acids approach complete dissociation; however, their ph depends on the concentration of the strong acid. Consider a solution of 0.1 M HCl (since strong acids like HCl completely dissociate, we can assume the [H + ] = 0.1 M). We can then calculate the ph of this solution: ph = log 10 [H + ] = log 10 (0.1) = log 10 (10 1 ) = ( 1) = 1. Note: strong acids have large K a values ( 10 2 ) and small pk a values ( 2.0) whereas weak acids have small K a values and large pk a values. 8. All salts (e.g NaCl; KCl) are completely dissociated in dilute aqueous solutions. V. FUNCTIONAL GROUPS: Structure Name Stability ester phosphate ester Stable, but reactive. Biologically requires energy to form esters; cleaved by lipases. Also cleaved in acidic or basic solutions. Stable, but reactive. Biologically requires energy to form phosphate esters; cleaved by phosphatases. Cleaved chemically with strong acids. R-CH 2 -O-CH 2 -R ether Very stable R-CH 2 -S-CH 2 -R thiol ether Very stable R-CH 2 -SH thiol More reactive than their alcohol analogs. R-CH 2 -S-S-CH 2 -R disulfide Stable, but reactive. Formation from two thiol groups is an oxidation reduction reaction, with the disulfide being the more oxidized functional group. Reaction is readily reversed hemiacetal hemiketal using reducing agents. Unstable, unless it forms a cyclical hemiacetal (i.e. carbohydrates, like glucose, favor the cyclical hemiacetal structure in water). Unstable, unless it forms a cyclical hemiketal (i.e. carbohydrates, like fructose, favor the cyclical hemiketal structure in water). 7 P age

8 Structure Name Stability halide (chloride, bromide, iodide, fluoride) Can react with amines to form secondary amines secondary amine Very stable NH NH 2 + C NH 2 guanidinium Retains positive charge at ph values above 10.5 phenyl Very stable phenol Can ionize to O at high ph benzyl Very stable indole Decomposes in acid; stable in alkali N NH imidazole Can accept a proton at neutral ph to become: =NH + 8 P age