Chapter 3 Notes
Chapter 3 Notes 87222 - BCHM 3050 - 002
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This 6 page Class Notes was uploaded by America Seach on Wednesday January 27, 2016. The Class Notes belongs to 87222 - BCHM 3050 - 002 at Clemson University taught by Srikripa Chandrasekaran in Spring 2016. Since its upload, it has received 27 views. For similar materials see Essential Elements of Biochemistry in Biology at Clemson University.
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Date Created: 01/27/16
Chapter 3: 3.1: Molecular structure of water - Polar: there is an unbalance in electron distribution - dipoles: molecules, such as water, in which charge is separated - hydrogen bond: hydrogen is unequally shared by the two electronegative centers - electrostatic interaction: occurs between any two opposite partial charges (polar molecules) or full charges (ions or charged molecules) - covalent bonds: involve electron sharing with orbital overlap or mixing 3.2: Noncovalent bonding - noncovalent interactions are usually electrostatic meaning that they occur between the positive nucleus of one atom and the negative electron clouds of another nearby atom - in living organisms, the most important are ionic interactions, van der Waals interactions, and hydrogen bonds - Ionic interactions: occur between charged atoms or groups are nondirected- they are felt uniformly in space around the center of charge; opposite charges attract, similar charges repel; the attraction of positively and negatively charged amino acid side chain forms SALT BRIDGES - Hydrogen bonds: in water each molecule can form hydrogen bonds with four other water molecules; bond is partially covalent and causes the force of attraction to have directionality - Van der Waals forces: relatively weak electrostatic interactions; electronegative atoms with unshared pairs of electrons are easily polarized 1. Dipole-dipole: occur between molecules containing electronegative atoms causing them to connect from the negative and positive ends; hydrogen bonds are strong 2. Dipole-induced dipole: a permanent dipole induces a transient dipole in a nearby molecule by distorting its electron distribution; weaker than dipole-dipole 3. Induced dipole- induced dipole: the motion of electrons in nearby nonpolar molecules result in transient charge imbalance in adjacent molecules; often called London dispersion forces which are very weak - Noncovalent bonds (ionic interactions and van der Waals forces) are important in determining the physical and chemical properties of living systems - Hydrogen bonds, with both dipole/dipole and covalent character, play a critical role in the properties of water and its place in the structure and function of cells 3.3: Thermal Properties of Water - Water is liquid at room temperature, and its melting and boiling points are high - Hydrogen bonding is responsible for its unique characteristics - The maximum number of hydrogen bonds form when water has frozen into ice; energy is required to break these bonds - Ice is less dense than water in its liquid state - When ice is warmed to its melting point, approximately 15% of hydrogen bonds break - Hydrogen bonding is responsible for water’s unusually high freezing and boiling points - Because water has a high heat capacity, it can absorb and release heat slowly. Water plays an important role in regulating heat in living organisms 3.4: Solvent Properties of Water - Water is the ideal biological solvent and it easily dissolves a wide variety of the constituents of living organisms - Hydrophilic molecules, cell water structuring, and sol-gel transitions: o Salts are held together by ionic forces o Because water molecules are polar, they are attracted to charged ions (either positive or negative) o Shells of water are known as solvation sphere and they cluster around positive and negative ions o The capacity of a solvent to reduce the electrostatic attraction between charges is indicated by its dielectric constant o Water is sometimes referred to as the universal solvent because of the large variety of ionic and polar substances it can dissolve and its large dielectric constant o When ionic compounds such as NaCl is dissolved in water, its ions separate because the polar water molecules attract the ions more than the ions attract each other. In reality, the solvation sphere of Na+ has four times the volume of that Cl- because of the higher charge density of the sodium ion o Sol-gel transitions: a gel is a colloidal mixture (consisting of biopolymers with polar surfaces in association with absorbed water); the stability of a gel is very dependent on the length and cross-linking of the polymer and continuity of the adsorbed water; changes in temperature, matrix architecture, and inclusion of solutes can lead to a transition from the gel to a “sol” or liquid state; transitions from gel to sol contributes to cell functions- most notably cell movements; a cell moves forward because of the coordination of sol-gel transition in the cell cortex(ectoplasm) and the cytoplasm in the cell’s interior(endoplasm)- a contractile force in the rear of the cell squeezes the fluid endoplasm forward o Hydrophobic molecules and hydrophobic effect: hydrophobic-water hating- molecules, such as the hydrocarbons, are insoluble in water; the hydrophobic effect is responsible for the generation of stable lipid membranes that contribute to the fidelity of protein folding o Amphipathic molecules: a large number of biomolecules ~amphipatic~ contain both polar and nonpolar groups; when they are mixed with water, they form structures called micelles in which the charged species (polar heads) have oriented themselves so they contact water and the hydrophobic tails are on the interior; allows for phospholipid bilayer to form o Water’s dipolar structure and its capacity to form hydrogen bonds enable water to dissolve many ionic and polar substances o Nonpolar molecules cannot form hydrogen bonds with water and are excluded via clathrate formation o Amphipathic molecules, such as fatty acid salts, spontaneous rearrange themselves in water to form micelles o Osmotic pressure: Osmosis: the spontaneous passage of solvent molecules through a semipermeable membrane Osmotic pressure: the pressure required to stop the net flow of water across a membrane; depends on the solute concentration; calculated by π= iMRT where π is osmotic pressure (atm), i is vant hoff factor, M is molarity (mol/L), R is the gas constant (0.082), and T is temperature in Kelvin The concentration of a solute can be expressed in terms of osmolarity Isotonic solution: the concentration of solute and water is the same on both sides of the selectively permeable membrane; there is no net movement in either direction HypOtonic solution: when cells are placed into a solution with a lower concentration, water moves into the cell; this causes the cell to swell and rupture through a process called hemolysis; what plants typically exist in, rigid cell walls prevent the cells from bursting HypErtonic solution: when cells are placed in solutions with higher solute concentrations, the cell shrivels because there is a net movement of water out of the cell; this process is called crenation; the cell membrane pulls away from the cell wall because of water loss and the plant wilts Macromolecules have little direct effect on cellular osmolarity because their cellular molar concentration are relatively low Membrane potential: the electrical gradient established because of asymmetry on the surface of cell membranes; it provides the means for electrical conduction, active transport and even passive transport o Osmosis is the movement of water across a semipermeable membrane from a dilute solution to a more concentrated solution o Osmotic pressure is the pressure exerted by water on a semipermeable membrane as a result of a difference in the concentration of solutes on either side of the membrane 3.5: Ionization of water - A solution that contains equal amounts of H+ and OH- is said to be neutral; when it has excess H+, it is acidic; when it has excess OH-, it is basic - Acids, Bases, and pH: o Strong acids and bases ionize almost completely in water; separate completely o Weak acids: organic acids (compounds with carboxyl groups) do not dissociate completely in water o Weak bases: organic bases have a small but measurable capacity to combine with hydrogen ions; many contain amino groups o Conjugate base: the deprotonated product of the dissociation reaction (will have a negative charge) o Strength of a weak acid (capacity to release hydrogen ions) can be determined by finding the Ka or dissociation constant---- Ka= [H+][A-] ÷ [HA] The larger the Ka value, the stronger the acid Use pKa=-log(Ka) to find it on a logarithmic scale; the smaller the value of the pKa, the stronger the acid o To find the pH using hydrogen ion concentration: pH= -log[H+] or [H+]= 10^(-pH) o pH 7 is neutral and has [H+] equal to 1x10^-7, below 7 is acidic and [H+] greater than 1x10^-7, above 7 is basic/alkaline - Buffers: help to maintain a relative constant hydrogen ion concentration; most common buffers consist of a weak acid and their conjugate base; resist changes to pH o Acidosis: a condition that occurs when human blood pH falls below 7.35; results from excessive production of acid in the tissues; the CNS becomes depressed and can cause a coma or death o Alkalosis: a condition that occurs when pH goes above 7.45; overexcites the CNS and muscles go into spasmatic attack; if not corrected, it can cause convulsions and respiratory arrest o Le Chatelier’s principle: states that if stress is applied to a reaction at equilibrium, the equilibrium will be displaced in the direction that relieves the stress o A buffers capacity to maintain a specific pH depends on 2 factors: 1. The molar concentration of the acid-conjugate base pair 2. The ratio of their concentrations o Henderson-Hasselbalch equation: pH= pKa + log [A-]/[HA] - Liquid water molecules have a limited capacity to ionize to form H+ and OH- ions - The concentration of hydrogen ions is a crucial feature of biological systems primarily because of their effects on biochemical reaction rates and protein structure - Buffers, which consist of weak acids and their conjugate bases, prevent changes in pH (a measure of [H+]) - Weak Acids with more than ONE ionizable group: some acids can donate more than one hydrogen ion o use titration to show each single proton leaving o at a low pH, most molecules are fully protonated; as a strong base (NaOH) is added, protons are released in the order of decreasing acidity, with the least acidic proton (largest pKa value) ionizing last - Physiological buffers: three most important in the body are bicarbonate buffer, the phosphate buffer, and the protein buffer o Bicarbonate buffer: most important in the blood; has three components Carbon dioxide reacts with water to form carbonic acid, Carbonic acid dissociates to form H+ and HCO3- ions (bicarbonate) o Phosphate buffer: consist of the weak acid-conjugate base pair H2PO4- and HPO4^(2-) Does not have a major effect in the blood Important in extracellular fluids o Protein buffer: composed of amino acids linked together by peptide bonds, proteins contain several types of ionizable groups in side chains that can donate or accept protons; since protein molecules are highly present in living organisms, they are powerful buffers; hemoglobin and blood pH
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