Exam1 StudyGuide Biochemistry I
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This 9 page Study Guide was uploaded by Spurthi Pasham on Saturday July 16, 2016. The Study Guide belongs to Biochemistry I at University of Texas at Dallas taught by Mehmet CandasJiyong Lee in Summer 2016. Since its upload, it has received 63 views. For similar materials see Biochemistry I in Biochemistry at University of Texas at Dallas.
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Date Created: 07/16/16
BIOL/CHEM 3361 - BIOCHEMISTRY I SUMMER 2016 EXAM 1 STUDY GUIDE 1) * What is the attraction force related to the hydrogen bonds within liquid water? Dipole-Dipole Force. (H-Bonding) 2) * What extent/how much do weak acids ionize in aqueous solution? Weak acids are partially ionized. Each pH unit above the pKa of an acid results in a 10-fold increase in the ratio of ionized to non-ionized compound. Conversely each pH unit below the pKa of an acid results in a 10-fold increase in the ratio of non-ionized to ionized compound. Not completely- the extent depends both upon the pH of the solution and the nature of the acid in question. 3) * What type of intermolecular bonds can a carboxylic acid form at pH 7.4? Carboxylic acid (including those found in amino acids) are deprotonated at pH 7.4 - which is what gives many amino acids their neutral (zwitterionic) characteristic at that pH. As such, they cannot form hydrogen bonds, and so are relegated to ionic bonding (as in soaps of fatty acids), dipole interaction (due to the net negative region created by the two oxygen atoms) and Van Der Waals forces. 4) * What is an amphiphilic molecule? An amphiphilic molecule is a molecule containing both a hydrophobic and a hydrophilic region, as in the case of fatty acids. This is not to be confused with an amphoteric species, which can act as either an acid or a base. Amphiphilic molecules interact favorably with both polar and nonpolar environments AMPHIPATHIC molecules are the ones that contain both polar and nonpolar groups. (both the same thing) 5) * What is a buffer? A buffer is usually composed of a weak acid and its conjugate base. This combination creates an atmosphere which resists pH change to a certain degree indicated by buffer capacity, which is defined as the change in acid or base volume (added to solution) over the change in pH. This mechanism is achieved by the conjugate base in solution neutralizing added acid, and by the acid itself neutralizing added base, such that changes in the amounts of free hydrogen ions or hydroxide groups is minimized. The pKa of the weak acid should be close to the desired pH. *Buffers are most effective in the range pH=pKa +/- 1. 6) *What will be the pH of a 0.1M solution of sodium acetate? Since sodium acetate is the salt of acetic acid (it accepts a proton from water to produce acetic acid and hydroxyl ions), we need to find the pKb, then Kb, [OH⁻], pOH, and pH. Acetic acid’s pKa = 4.76; Ka = 1.75 x 10 . -5 NaCH CO3 + H OCH C2OH + 3H + Na - + pKw = 14 = pka + pKb; pKb = 14 - 4.76 = 9.24 Kb = 10 -9.= 5.75 x 10 -10 5.75 x 10 = [CH3COOH][OH-][NaCH3COO]= x2[0.1 M] x2= 5.75 x 10 ; x = 7.59 x 10 = [OH]-6 - pOH = -log(7.59 x 10 ) = 5.12 pH = 14 - 5.12 = 8.88 7) * What is the ratio of citric acid (pK1 = 3.09) to monosodium citrate in a 1.0 M citric acid solution with a pH = 2.09? it is a buffer, its pH=2.09 citric acid is an acid (pk1=3.09) mono sodium citrate is salt pH=pk1+log salt/acid 2.09=3.09+ log salt/acid log salt/acid=2.09-3.09 log salt/acid =-1 salt(monosodium citrate )/acid(citric acid)=10 -1 The ratio between monosodium citrate and citric acid = 0.1 which is 1/10. Since it’s the ratio of acid to base, this needs to be inverted, leading the answer to be 10 M to 1 M. 8) * How many hydrogen bonds are formed per water molecule? 2.3 in water not 2 (liquid) 4 H bonds per water molecule in ICE (solid) 9) * Why do hydrophobic interactions occur? Water tends to organize itself in such a way so as to form hydrogen bonds between its molecules. A hydrophobic molecule, when introduced to water, interrupts these interactions and forces the water to reorganize so as to optimize its auto-bonding (into a cagelike structure that surrounds each solute molecule called clathrate form). Concordantly, hydrophobic molecules tend to become clustered with each other whereupon their long, nonpolar hydrocarbon chains ‘attach’ to each other weakly as a result of small induced dipoles within their electron clouds also known as Van Der Waals interactions. 10) * What is the ranking order of weak bonds (strong to weak)? They vary so they can’t be ranked in terms of strength, but if you had to... 1. Hydrophobic Interactions: <40 kJ/mol 2. Ionic Interactions: 20 kJ/mol 3. Hydrogen Bonds: 12-30 kJ/mol 4. Van der Waals Interactions: 0.4-4.0 kJ/mol 11)* How would you compare the strength of hydrogen bond to covalent C- C or C-H bond? Using their bond energies? H-H 436kJ/mol, C-H 414kJ/mol, C-C 343kJ/mol Comparing bond energies confirms that Covalent bonds are stronger than hydrogen bonds. 12) What is the entropy relationship between hydrophobic interactions and water? Hydrophobic interactions increase “order” of water, which will decrease entropy. 13) *What are the properties of water in ice form? •Ice: 4 H bonds per water molecule •Ice: H-bond lifetime - about 10 microsec (10^-6) Forms lattice structure 14)* Why is ethanol exceptionally soluble in water? Ethanol (c2h6o) is polar because it contains a hydroxyl group that can form hydrogen bonds with water. “Like dissolves like,”so a polar substance like ethanol will be miscible in water. Also it doesn’t have a long hydrocarbon chain which could contribute to hydrophobicity and reduce its solubility in water. 15)* What is the ionization constant of water Kw at 25°C? 1.00 x 10¯ 14 16)* What is the significance of pH at the midpoint of an acid/base titration? At the half-equivalence point/midpoint of an acid/base titration, the ratio of the concentration (M) of acid to base is one and, therefore, the base ten logarithm of that ratio is zero. This allows the Henderson-Hasselbalch equation to be simplified to the form pH = pKa. Equivalence point: Moles of titrant = moles of unknown concentration; above answer is for the half equivalence point. midpoint=half equivalence point 17) * What is the basis of the blood buffering system? bicarbonate/carbonic acid coupling (pg 45) The carbonic/bicarbonate buffering system work together to control the blood’s pH. 18) * How are the supramolecular biological complexes (assemblies) of multiple components held together? Since supramolecular complexes are held by weaker bonds that are easily reversible, noncovalent interactions such as hydrogen bonds, hydrophobic forces, van der Waals forces, and ionic interactions hold them together. Supramolecular complexes form when one or more of the classes of macromolecules come together to form specific assemblies that serve subcellular functions. Their structural integrity is maintained by noncovalent forces including hydrogen bonds, ionic attractions, Van Der Waals forces, and hydrophobic interactions between macromolecules. Although these are weak forces, they are numerous in these assemblies and collectively maintain the functional state. 19) * What is the structural basis of molecular recognition in biology? Biomolecular recognition is mediated by weak chemical forces. The principle of structural complementarity is the very essence of biomolecular recognition (i.e. a protein recognizes a specific metabolite, a strand of DNA recognizes its complementary strand, sperm recognizes an egg) 20)* What is the importance of weak forces in biology? Influence the structure and behaviors of all biological molecules, create interactions that are constantly forming and breaking under physiological conditions, restrict organisms to a narrow range of environmental conditions. The lower energy of intermolecular forces makes it so that interactions between molecules can be changed without the large energy investment it takes to break covalent bonds. 21) * What can ∆G tell about a process? (consider ∆G = 0; ∆G > 0; ∆G < 0) Delta G indicates the spontaneity of a reaction under a specified set of conditions, namely pressure and temperature. When ∆G = 0 then the process is at equilibrium and there is no net flow either in the forward or reverse direction. When ∆G < 0 the process proceeds spontaneously in the direction written. When ∆G > 0 the reaction proceeds in the reverse direction. 22*) What is ∆G⁰? ∆G° = -RTlnKeq at equilibrium Delta G prime denotes the free energy change of a reaction which occurs specifically at standard temperature and pressure conditions (1M concentration, 1 atm pressure, 25 Celsius) ΔG° = ΔH° - TΔS° 23) * How does ∆G relate to the tendency, direction, and reversibility of a reaction? See #21 :) Reversing the reaction reverses the sign of delta G. 24)* Life is a process; then what would you say about the overall ∆G of life? ΔG more negative than -25kj/mol The change in free energy of all of the biochemical processes in life is constantly transferring from one state of energy to another. Following the first law of thermodynamics, energy is neither created nor destroyed. Energy changes may be spontaneous or require work to continue in a certain direction. Consider that the transfer of the energy in the living systems is a non-spontaneous coordination of several spontaneous processes. 25)* How does disorderness in/of a system affect T∆S? In the equation of ∆G = ∆H - T∆S, temperature and disorderness of a system (aka entropy, ∆S) are directly proportional. When ∆S increases, it is because temperature is increased as a constant, and vice versa. 26) * What is the effect of enzyme catalysis on ∆G? * Enzyme catalysis, like all catalysis, has no effect on the delta G of a reaction. Rather, catalysts act to stabilize the transition states of molecules in reaction, thereby lowering the activation energy of the reaction and allowing the reaction to proceed at lower cost (less energy investment) and a faster rate. 27) *How do enzymes accelerate biochemical reactions? Specific modalities of action vary but enzymes act in general to stabilize the transition states of molecules in reaction and thereby lower the activation energy of the reaction. 28) What is a van’t Hoff plot? A Van’t Hoff Plot is a method of graphing a thermodynamic scenario such that the equation produced by the best fit line presents the natural logarithm of the equilibrium constant as being proportional to the temperature and entropy change of a reaction with temperature taken into account. Furthermore, that relationship is presented in the slope-intercept form of a line and the equation can be derived by setting the kinetic and thermodynamic equations for delta G equal to one another and solving for the natural logarithm of the rate constant. lnKeq = - ΔH/R(1/T) + ΔS/R 29) * What is the relationship (equation) between Keq and change of standard free energy? See previous. ∆G°G͐ = -RT ln Keq at equilibrium 30) * Are biological organisms isolated, closed, or open system? Open systems, as energy and matter are exchanged with the surroundings. 31) *How is the equilibrium constant of a reaction related to the change in free energy of the reaction? ∆G = ∆G° + RT ln Q ∆G =-RT ln Keq 32) * Is the change in enthalpy (∆H) for the complete oxidation of a fatty acid via a biochemical pathway different than sudden combustion of that fatty acid to CO2 and H2O? No , it is the same, the same amount of energy is contained within the bonds. 33) * What is the energy level of a reaction at its equilibrium? Highest? Lowest? Zero? Lowest When delta G equals 0, the process is at equilibrium and there is no net flow in the forward or reverse direction. 34)* What happens to the direction of a reaction at equilibrium if the concentration of reactants or products are changed? If product concentrations are increased, the equilibrium will shift left. If reactant concentrations are increased, the eq will shift right. If product concentrations are decreased, eq shifts right. If reactant concentrations are decreased, eq shifts left. = System moves to oppose the change in conditions 35) *How do the thermodynamically unfavorable reactions occur in biological systems? Thermodynamically unfavorable reactions occur via reaction coupling (pairing an unfavorable reaction with a favorable one) Ex. hydrolysis of ATP 36) * Is the formation of peptide bond thermodynamically favorable? Peptide bond formation during protein synthesis is a dehydration reaction, which requires input of energy; therefore it is NOT thermodynamically favorable (spontaneous). 37) * Which atoms of the amino acids are contained within the amide plane of the peptide backbone? Carbon, Nitrogen, Hydrogen, Oxygen 38) * Which amino acids would most likely be found on the surface of proteins? Those with hydrophilic (polar, positively charged) side chains: Arginine (R), Histidine (H), and Lysine (K) Plus the acidic aspartic and glutamic acids, plus the polar amino acids being serine, threonine, asparagine, glutamine, tyrosine, and cysteine. (per the T.A) 39)* Is there any amino acid stereoisomer preference in protein biosynthesis/translation process? Yes, most amino acid residues are in the L form and are specifically complementary to active sites of other molecules in order to function. The D form of an amino acid will not bind at all, thus biosynthesis will not proceed. 40) * Which type of amino acid stereoisomers (D or L) occur in most proteins? L form 41)* Which amino acids is not chiral? Glycine 42) * What is a zwitterion form of an amino acid? Neutral, amino acid has both and positive and negative electrical charge making it neutral. Amino acid present at PI (isoelectric point)= zwitterion. 43) * What happens to carboxylic acid group of an amino acid at physiological pH? Carboxylic acid is deprotonated (pH>pka) at the ph 7.4, giving the amino acid a zwitterionic characteristic (because the other side is NH3+ and they balance each other out, but only if a charged side chain isn’t present) 44) Know the names (including three letter, and single letter denotations), structures and properties of each of the 20 amino acid in terms of their polarity, hydrophobicity, acidity, and charge. 45) What is the difference between serine and homoserine? Homoserine (also called isothreonine) is an α-amino acid with the chemical formula HO CCH2NH )CH C2 OH2 It2differs from the proteinogenic amino acid serine by insertion of an additional -CH - u2it into the backbone. Serine contains an α-amino group (which is in the protonated −NH +3 form under biological conditions), a carboxyl group (which is in the deprotonated – COO − form in physiological conditions), and a side chain consisting of a hydroxymethyl group (see hydroxyl), classifying it as a polar amino acid. Instead of ch2oh r group, there’s a ch2ch2oh r group 46) * Why do histidine residues act as a good proton donor and acceptor in many enzyme catalyzed reactions? The pKa of Histidine is close to neutral (6.1), thus it has the ability to act either acidic or basic and donate or accept protons because the physiological pH is within its buffering range 47) How does the presence of an amine group affect the pKa of the α−carboxyl group of an amino acid? The pKa on an isolated amino group is 9 (as for example, the side chain amino group of lysine whose pKa = 10.5. In general, the pKas of a amino groups in the amino acids are around 9.5. Thus, the proximity of the a carboxyl group lowers the pKa of the a amino group. Inversely, the presence of an amine group will increase the pKa of the a- carboxyl group, which is around 2-2.3. 48) What is the product of a reaction between an amino acid and aldehyde? a. amide. b. Hemiacetal c. substituted amide. d. ester e. Schiff base. Answer has to be either a,b,c,d,e (I’m not sure which one) i think C? 49) * Which amino acids absorb light at 280 nm? (250- 280 is UV light don’t get tricked) Ultraviolet light is absorbed well by conjugated systems of double bonds. Since the wavelength of 280nm falls within the range of ultraviolet light, it should be expected that those amino acids containing conjugated double bond systems will best absorb light at 280nm. Those amino acids would be phenylalanine (F), tryptophan (W) and tyrosine (Y) since those are the three nonpolar, aromatic amino acids. Tyrosine is a polar, uncharged amino acid, but still absorbs UV light better than phenylalanine.
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