Bonds
Order the following bonds from highest in strength to lowest in strength: Hydrogen, covalent, Van der Waals, and ionic.
Covalent>ionic> hydrogen>Van der Waals
What does every variable stand for in the equation ΔG= ΔH-TΔS?
ΔG= spontaneity; ΔH= enthalpy or heat and ΔS= entropy or disorder.
What is being oxidized in the following reaction? Fe3+ + Cu+ à Fe2+ Cu 2+
Cu+
List at least two differences between DNA and RNA
RNA has a hydroxyl group on the 2’ carbon, DNA has a H. DNA uses Adenine and oxygen uses uracil.
Give an example of each of the following bonds. Covalent, hydrogen, Van der Waals, ionic
Covalent: DNA polymer formation; hydrogen: water binding to other water molecules; Van der Waals: stabilizing DNA double helix; Ionic: NaCl
True or false, when enthalpy is negative and entropy is positive, the ΔG is always negative.
True; this is because of the equation. Subtracting a positive number from a negative number is always negative.
Define the reducing agent and oxidizing agent for the given reaction
2Na (s) + Cl2 (g)à NaCl .
oxidizing agent Cl-; Reducing agent Na+
In Adenosine 5’- monophosphate, how many phosphates are there and what is the base?
one phosphate and adenine
List at least three properties of water.
Water is polar, water is capable of forming more than one hydrogen bond, can lead to the hydrophobic effect, has a high dielectric constant, high specific heat, cohesion and adhesion.
What does it mean for the reaction if the Gibb’s Free energy is equal to zero?
the reaction is at equilibrium
Determine the E0’ for the oxidation of ethanol by the common biological oxidant nicotinamide adenine dinucleotide (NAD+):
Ethanol + NAD+ à acetaldehyde + NADH + H+
NAD+ + H+ + 2e- à NADH E0= -0.315 V
Acetaldehyde + 2H+ + 2e- à ethanol E0=-.197V
-.315V – (-.197V) or -.315V + 0.197V = -0.118V
List the purines and the pyrimidines
Purine: adenine and guanine. Pyrimidines cytosine, uracil, and thymine.
Describe the hydrophobic effect and how it relates to lipid bilayers.
The hydrophobic effect is the exclusion of nonpolar substances from an aqueous substance from an aqueous solution. It active in the bilayer because as the polar side of the bilayer aggregates toward the aqueous solution while the nonpolar tails aggregate towards the middle.
Is it energetically favorable for mercury to melt at 263 K (-10 ˚C), where ΔH is +5630 J/mol and ΔS is +20.6 J/K•mol?
ΔG= ΔH-TΔS= 5630J/mol – 263K (20.6 J/Kxmol) = 212 J/mol unfavorable.
What is the standard free energy change if the E0 = -0.118V
ΔG- -nFΔ E0 = (-2) (96485 J/mol*V) (-0.118V) = + 22.8kJ/mol or 22800 J/mol
List at least three kinds of bonds in DNA and describe where they are found.
hydrogen, between nucleotides; phosphodiester bridge together the backbone; glycosidic link together the base and the sugar.
Consider an acetic acid buffer (pKa = 4.76) containing 3 M HOAc and 3 M Na+OAc. Now add 0.5 mol of HCl (strong acid) to 1.0 liter of this buffer; H+ reacts quantitatively with OAc– to drive the pH down. Calculate the pH
pH = pKa + log[3 M/3 M] = 4.76
HCl + OAc– = HOAc + Cl-
This reaction consumes one OAC– and produces one HOAc
[HOAc] = 2 M + 0.5 M = 2.5 M
[OAc–] = 2 M – 0.5 M = 1.5 M
pH = 4.76 + log(1.5/2.5) = 4.76 – 0.087 = 4.538
A reaction is setup at equilibrium and has a DG* = +2.3 kJ/mol. The concentration of product is 5mM. What is the concentration of the product?
K= e^(-2300/8.314x298) = .395 = Product [5mM] / reactant [x]. x = 12.66
If you know the ΔG of a reaction, what else would you need to calculate the enthalpy?
Temperature and ΔS
List and describe the four components of PCR
Template: contains the DNA sequence of interest
Primer: short single stranded DNA molecules that contains part of the target sequence
dNTPs: A, T, G, C nucleotides
Polymerase: the enzyme that catalyzes the phosphodiester bond formation