Quiz 1 Study Guide: DNA & RNA, Amino Acids, Bonds, Structures

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Biochemistry & Molecular Bio.
David Gross

Here are some very brief guidelines as to what I would like you to know for Quiz 1. Chapter 1 •The meanings of ∆G, ∆H and ∆S • ∆G is called Gibbs free energy and is is composed of both enthalpy and entropy. • ∆H is the component enthalpy and is the equivalent to the heat content of the system in question. • ∆S is the component entropy and is a measure of how the energy is dispersed within the sytem in question (a measure of a system’s disorder or randomness). •The implications of the equation ∆G = ∆H -T∆S for biological reactions • T represents temperature in Kelvin and is a coefficient of entropy because entropy varies with temperature, entropy increases when it’s warmed because thermal energy has dispersed throughout the system. • When heat is released from a system ∆H < 0, and when energy is absorbed ∆H > 0. • Similarly ∆S can be both posative and negative. •Spontaneous and nonspontaneous reactions • For a spontaneous reaction ∆G < 0, for a nonspontaneous reaction ∆G > 0. •Oxidation state and reactivity • Reduction is achieved by the gain of electrons through the addition of hydrogen or the removal of oxygen. • Oxidation is the loss of electrons through the addition of oxygen or removal of hydrogen. •Bacteria (eubacteria), Archaea (archaebacteria), Eucarya (eukaryotes) and the evolution of cellular structure • Life began through polymerization from inorganic molecules • Organic molecules formed into photosynthetic organisms that could photosynthesize • Natural selection would favor those organisms that could replicate and were contained in membranes • The rise in oxygen levels would have forced these organisms into microenvironements that had a lesser oxygen concentration • Present day organisms are of two types: o Prokaryotes: small unicellular organisms that lack a nucleus and don’t usually contain an internal membrane system. And also Archaea: organisms that inhabit exteme environments, but are found most everywhere o Eukaryotes: usually larger than prokaryotic cells and contain a nucleus and membrane-bound cellular compartments. They may be unicellular or multicellular. • Eukaryotic cells probably developed from prokaryotic cells which grew together to form the structures found within a eukaryotic cell. • This would have allowed for the division of labor within the cell and consequent development of multicellular organisms. Chapter 2 •Properties of water: polarity and the ability to form hydrogen bonds (H bonds) • The molecule has tetrahedral geometry • Central oxygen atom has two unshared electron pairs • Molecule is charged with oxygen bearing the negative charge and both hydrogens bearing posative charges • Neighboring water molecules will orient themselves so that the partially positive hydrogen atoms align with the partially negative oxygen atom to form a hydrogen bond • Each water molecule can engage in four simultaneous hydrogen bonds, two with the hydrogen atoms and two with the unpaired electrons on the oxygen atom • Hydrogen bonding gives water the ability to form a crystalline structure in ice •Noncovalent bonds in macromolecular structure • Though covalent bonds define molecular constitution, noncovalent bonds, though weaker, govern the final 3D structure H bonds • Second strongest noncovalent bond, forms between H attached to O, S, or N and forms between open O, S, or N Ionic bonds • Form between two ions, the stongest noncovalent bond. van der Waals interactions • Also known as dipole-dipole interaction, the weakest noncovalent bond, forms between two stongly polar groups. •Aqueous solutions solubility of ionic and polar molecules; effect of dielectric constant • Dielectric constant is the measure of a solvent’s ability to diminish the electrostatic attraction between dissolved ions, water has a high dielectric constant • molecules with polar or ionic functional groups are readily solubilized hydrophobic effect • molecules that lack polar groups are insuluble in water and said to be hydrophobic • The exclusion of nonpolar substances from an aqueous solution is the hydrophobic effect relationship to formation of internal core of globular proteins • hydrophobic molecules will be in the center of globular proteins relationship to formation of micelles, vesicles and membranes • Amphiphilic molecules will form these with the hydrophillic head on the outside and hydrophobic tail in the center of a bilayer •Acid-base chemistry pH and pK; definitions • pH is the measure of the hydrogen ion concentration, pH=-log[H+] • pK is the convinient form of the acid dissociation constant Ka, pK=-log[Ka] How to use Henderson-Hasselbalch Equation • This relates the pH of a solution to the pK of an acid and the concentration of the acid (HA) and its conjugate base (A-), pH=pK+log([A-]/[HA]) usefulness of weak acids (and bases) for buffers • When a stong acid such as HCl is added to water with a weak acid in equilibruim, the pH doesn’t change dramatically because some of the added protons combine with the conjugate base to re-form acid and therefore don’t contribute to an increase in pH, same goes when using bases as buffers Chapter 3 •Experimental basis for model of DNA double helix (in a very general sense) Chargaff's rules • A & T and G & C are present in the same concentrations in DNA Franklin's x-ray crystallography • Showed that DNA was in a double helix form •Know chemical structure of bases, nucleosides and nucleotides found in DNA and RNA • Bases o • Nucleosides o • Nucleotides o •Chemical structure of nucleic acids, i.e., the phosphodiester backbone • phosphodiester backbone o •Base pairing and base stacking in the formation and stability of double-stranded DNA and RNA • A:T & G:C • Base pairs are 11A wide reguardless of the pair • In DNA bases stack 3.4A apart •Properties of DNA double helix • single turn is 34A (10 bp) • The entire helix is 20A wide • There is a major and minor groove • It’s twisted in a right hand fashion • The sugar phosphate backbone is on the outside and binds with Mg2+ ions in solution to minimize the negativity of the backbone and stabalize it • The core of the helix is solid because of base stacking •Peculiarities of RNA secondary (base-pairing) and tertiary (three-dimensional) structure • RNA usually single stranded • can fold back on itself so that base pairs form between complementary segments of the same strand • Can also bind a ssDNA to form RNA-DNA hybrid helix o wider and flatter than DNA double helix (26A wide)
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