Lecture 1: Introduction, Noncovalent Interactions, and ...cbc.chem.arizona.edu/.../spring/460web/lectures/LEC1_Intro_Water.pdf · biological milieu is primarily aqueous -- water is

01/14/2007 06:40 PMLEC1_Intro_Water

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Lecture 1: Introduction, Noncovalent Interactions, and Water [PDF]

Reading: Berg, Tymoczko & Stryer: Chapter 1 problems in textbook: chapter 1, pp. 23-24, #1,2,3,6,7,8,9,10,11; practice problems at end of Gen Chem Review Updated on: 1/14/07 at 6:30 pm (added Objectives section on pp. 1-2 as a study guide; if printing PDF, just re-print pp. 1 and 2;nothing else was changed.]

Key ConceptsCELLS -- important structural features and compartmentalization (plasma membrane, nucleus or nucleoid, cytoplasm,ribosomes, organelles like mitochondria, chloroplasts, endoplasmic reticulum and Golgi apparatus)

3-D STRUCTURES of biomolecules determine their FUNCTIONS -- role of NONCOVALENT INTERACTIONS instructure and function.

Chemical unity of living systems

Chemistry of biomolecules -- functional groups, condensation reactions

Noncovalent interactions (hydrogen bonds, ionic interactions, van der Waals interactions, and "hydrophobicinteractions") are individually much weaker than covalent bonds, but are absolutely crucial to the structure and functionof biomolecules.Properties of water are crucial to understanding the properties (structural and functional) of biomolecules because thebiological milieu is primarily aqueous -- water is the solvent for most biomolecules.Most biomolecules have functional groups that are weak acids or bases, and the ionization properties of those groups arecrucial to the structures and functions of the molecules; the pH determines the state of ionization of biomolecular weakacids and bases.Biological systems, intracellular and extracellular, are BUFFERED.

OBJECTIVESReview (from posted lecture notes here) functional groups important in biomolecules, and condensation reactionsinvolving some of these functional groups.Identify on a drawing of a typical cell basic structural features found in all cells (nucleus or nucleoid, plasma membrane,cytoplasm, ribosomes); also identify mitochondria, chloroplasts, and the endoplasmic reticulum in a eukaryotic cell.List and explain the characteristics of 3 types of noncovalent bonds important in structures and interactions ofbiomolecules. Answer the following questions:

a) What is an ionic interaction (charge-charge interaction), and what other terms are used to describe the samething? How does the distance between two charged groups affect the energy of their interaction? What are therelative values of the dielectric constants for a nonpolar solvent and a polar solvent? How does solvent polarityaffect strength of ionic interactions? What type of solvent is water? Is an ionic interaction stronger in a polarsolvent or in a nonpolar solvent?b) What is a hydrogen bond, what is a hydrogen bond donor, and what is a hydrogen bond acceptor? How does thestrength of a hydrogen bond relate to its directionality? Be able to identify chemical groups (and the specificatoms involved) which can serve as hydrogen bond donors and groups which can serve as hydrogen bondacceptors. [Do not confuse a hydrogen bond donor with a proton donor (Bronsted acid).]



c) What are van der Waals interactions? How (qualitatively, not an equation) does their strength relate to thedistance between atoms? Why are such weak, nonspecific interactions important in biochemistry?

Explain hydrophobic "interactions" and explain the roles they play in biological systems (roles will become moreapparent as the semester progresses).Explain the properties of H2O (its polarity, hydrogen bonding ability, and solvent properties) that are so important to itsrole as the major constituent of living systems.Explain: buffer, pKa (and relate the strength of a weak acid to its pKa), and titration curve.Write out the 3 acid dissociation reactions of phosphoric acid, and write out condensation reactions showing formation ofa phosphomonoester and of a phosphodiester.Explain relationships between (and be able to do calculations involving):

a) [H+] and pHb) Ka (acid dissociation constant) and pKac) ratio of [conjugate base]/[conjugate acid] and pH and pKad) ratio of [conjugate base/[conjugate acid] and fraction or percent of a functional group that's in the form of theconjugate acid or conjugate base. (See practice problems at end of Gen Chem Review notes.)

BIOCHEMISTRY: the chemistry of life processes (reactions and interactions between biomolecules)

Fundamental concepts involved in biochemistry: 1. Space (structure, proximity) 2. Time (dynamic, interacting processes, rates of reactions) 3. Energy (thermodynamics) 4. Organic chemistry (and a bit of inorganic)

SPACE (1 Å = 10-10 m = 0.1 nm): •Bonds 1.5-3.0 Å •Molecules 5-100 Å •Aggregates 100-1000 Å •Cells 104-105 Å

TIME •Photosynthesis, vision: picoseconds (10-12 s) •Protein motion: nanoseconds (10-9 s) to seconds •Enzymes (reaction rates): microseconds (10-6 s) to seconds •Cell division: 103-105 s

FLUX: A --> B --> C Living systems in a DYNAMIC STEADY STATE •different from equilibrium state, which has NO NET FLUX •concentrations of A, B, C constant, but there's FLUX (flow of matter and energy) through system

ENERGETICS (thermodynamics) (Lecture 2) •free energy changes, enthalpy, entropy •reversal of disorder •reactions and interactions between molecules •covalent and noncovalent bond making/breaking •bond/interaction strengths

ORGANIC CHEMISTRY C, O, N, S, HBRIEF OVERVIEW OF CELL STRUCTUREfrom Nelson & Cox, Lehninger Principles of Biochemistry, 4th ed. (2004)

Nelson & Cox, 3rd ed. (2000) Fig. 2-1: Nelson & Cox, 4th ed. (2004) Fig. 1-6: Common



Universal features of living cells1) plasma membrane 2) nucleus or nucleoid3) cytoplasm

structural features of bacterial cells

Nelson & Cox, Fig. 1-7: 2 major types of eukaryotic cell, a) animal cell, and b) plant cell



CHEMICAL CONCEPTS (REVIEW)Nelson & Cox, Lehninger Principles of Biochemistry, 4th ed. (2004), Fig. 1-15: SOME COMMON FUNCTIONALGROUPS OF BIOMOLECULES



Note:H2O is a product of the following condensation reactions.Reverse reactions = hydrolysis reactions (H2O is added across the bond to split the molecule again.)



CHEMICAL BONDS

COVALENT BONDS: single, double, (triple)2 atoms share a pair of electrons to fill an orbital on each atom.Unequal sharing --> a polar molecule

1 atom has partial positive charge (δ+)



other atom has partial negative charge (δ–)e.g., O-H bonds

more equal sharing does NOT make a polarized bond(C–H bonds not polar)

NONCOVALENT INTERACTIONS: VERY important inlarge biomolecular structures (e.g. in proteins, nucleic acids .... )interactions between biomolecules (e.g. for processes of molecular recognition/specific binding, assembly of multimolecular structures like membranes andribosomes, .... )4 TYPES:

. 1 ionic interactions

. 2 hydrogen bonds

. 3 van der Waals interactions

. 4 hydrophobic effect/"interactions"from Nelson & Cox, Lehninger Principles of Biochemistry, 4th ed. (2004)

1. ionic interactions (salt links, salt bridges, ion pairs)

electrostatic attraction between oppositely charged groups (or repulsion between like charges)

Coulomb’s Law: Energy of interaction (strength of attraction or repulsion) = E



*q1 and q2 = charges of the 2 groups; opposite charges --> attractive force; like charges --> repulsive force*r = distance between the 2 groups (in denominator in equation, and squared) *D = dielectric constant of medium/solvent (also in denominator) *k = proportionality constant; value depends on units desired for expressing energy.

The higher the dielectric constant, the more polar the solvent:MEDIUM Dvacuum 1

hexane (very nonpolar solvent) 1.9H2O about 80

2. hydrogen bonds (These are also electrostatic in nature.)

interaction between

hydrogen atom covalently bonded to an electronegative atom, the DONOR group (–O–H or –N–H), andlone pair of non-bonded electrons on another electronegative atom, the ACCEPTOR group (:O=C, :O–H, :N–H, =N–, :O=P)Functional groups/atoms involved = hydrogen bond donors and hydrogen bond acceptors.ELECTRONEGATIVE ATOMS: O or N [NOT Carbon]Examples:DONOR ACCEPTOR

N–H•••••• :OO–H•••••• :NO–H•••••• :O

directionality of hydrogen bond important to its strength:Attraction between partial electrical charges strongest when the 3 atoms involved (e.g., –O–H ----- :O= ) lie in a straight line. However, sometimes structural constraints in biomolecules result in "bent" geometry (weaker hydrogen bonds).

Nelson & Cox, Lehninger Principles of Biochemistry, 4th ed., 2004, Fig. 2-5: Directionality of thehydrogen bond

3. van der Waals interactions (also electrostatic in nature, but much weaker than ionic interactions or hydrogen bonds.)

weak, nonspecific attractive force between ANY two atoms that approach within about 4-5 Å of each othermaximally attractive at the van der Waals contact distance (the sum of the radii of the atoms’ electron clouds), butif the electron clouds begin to overlap (too close approach), the force becomes strongly repulsive.Individually very weak and nonspecific, but sum of many close approaches is very important in steric(molecular shape) complementarity, which can be very specific.



Berg, Tymoczko & Stryer, Fig. 1.10: Energy of a van der Waalsinteraction as 2 atoms approach one another.

4. the "hydrophobic effect" (not really "bonding" at all)

tendency of nonpolar groups or molecules to associate (cluster together) to minimize exposure to H2O, the"oil drop effect"Hydrophobic "interactions" actually the result of the behavior/preferences of the H2O molecules

Water molecules are released from more ordered structures around the individual nonpolar groupswhen the nonpolar groups get together, permitting the H2O molecules to participate in more favorableinteractions with each other.

Berg, Tymoczko and Stryer, Fig. 1.12: The hydrophobic effect

Relative strength of different kinds of bonds/noncovalent interactions:(strongest) covalent >> ionic > hydrogen bonds > van der Waals (weakest)

Properties of H2O (extremely important in biochemistry; 55.5 M!)

polarity: Asymmetric charge distribution on H2O makes molecule POLAR.O atom δ– and H atoms both δ+, so molecule acts like a little magnet, a dipolar molecule.



Molecules without electronegative atoms, e.g. methane, hexane, etc., are nonpolar.hydrogen bonding: Each H2O molecule has an O atom with 2 unshared pairs of electrons so it can be theacceptor of 2 hydrogen bonds, and it also has 2 O–H bonds and can donate 2 hydrogen bonds as well.

thus each molecule can make a maximum of 4 hydrogen bonds to neighbors.Ice, solid H2O = crystal lattice type structure -- 4 hydrogen bonds per H2O moleculeLiquid H2O -- fewer hydrogen bonds per molecule (average of ~ 3.7), constantly forming and breaking

H2O molecules moving around in liquid, interacting with different neighboring molecules

Nelson & Cox, Lehninger Principles ofBiochemistry, 4th ed. (2004), Fig. 2-1a:

Polarity of H2O

Nelson & Cox, Lehninger Principles ofBiochemistry, 4th ed. (2004), Fig. 2-1c:Hydrogen bonding properties of H2O

Nelson & Cox, Lehninger Principles ofBiochemistry, 4th ed. (2004), Fig. 2-2:

Hydrogen bonding in ice

solvent properties: Because of its polarity and hydrogen bonding properties, H2O is an excellent solvent for manybiomolecules:

ionsother polar moleculesmolecules with groups that can hydrogen bond to H2OH2O (70% of the cell by weight) thus an excellent medium for most of the intracellular environment.However, H2O as a solvent

weakens interactions between oppositely charged ions (remember it has a high dielectric constant D), andcompetes with other solute molecules for hydrogen bonding groups in solutes.

Since concentration of H2O = 55.5 M, it competes very effectively indeed!Thus the core of membranes (permeability barriers between different aqueous compartments) consists of thenonpolar portions of lipid molecules, insoluble in H2O.

Furthermore, H2O would interfere/compete in many chemical reactions between biomolecules, so such reactions actuallyare catalyzed in binding "pockets" of macromolecules (active sites of enzymes) that H2O can’t get into.

Ionization properties of H2Oconcepts of pH, and proton dissociation equilibria of weak acids and bases (review your general chemistry on your ownor in special reviews provided for this course!)



SUMMARY:H2O and acids in aqueous solution dissociate to yield protons (H+), which in actuality would be hydrated to formH3O+.The tendency of an acid to donate its proton to H2O (dissociate the proton) can be quantitatively described by itsdissociation equilibrium constant Ka (or its pKa, which = –logKa).pKa values can be very accurately measured by titration curves, as the pH at half equivalence points.Relationship between pH, pKa, and ratio of [base]/[acid] can be described by the Henderson-Hasselbalch Equation:

Buffers:homeostasis: the maintenance of constant conditions in internal environmentFluids in living systems have a characteristic, almost constant, pH.How is pH controlled in living systems? By buffer systems.Buffer: aqueous system that tends to resist changes in pH when small amounts of acid or base are added. Buffer system: aqueous solution of a weak acid and its conjugate base Buffer range of a weak acid: near its pKa, about ±1 pH unit from the pKa. Maximum buffering capacity is atthe pKa.Equilibrium acid dissociation reaction (remember LeChatelier's Principle):

HA < == > H+ + A–

The higher the [H+] (i.e., the lower the pH), the more the equilibrium shifts to the left, so the moreconjugate acid will be present. Conversely, the lower the [H+] (i.e., the higher the pH), the more the equilibrium shifts to the right, so themore conjugate base will be present. Exact ratio of base to acid depends on the pH and the pKa: Henderson-Hasselbalch Equation

Remember that when pH = pKa, [A–] = [HA], so [base] /[ acid] ratio = 1/1 ([base] = [acid]). When pH = pKa, the “buffering capacity” of the mixture will be the greatest. That is, a given changein concentration of base (OH–) or acid (H+) will result in the smallest change in pH.

2 physiologically important buffer systems:1) INTRACELLULAR

inorganic phosphate ion (H2PO4– <--> HPO4

2–, pKa ~ 7) organic phosphates, e.g. phosphomonoesters (R-OPO2OH– <--> R-OPO3

2–, pKa ~ 7) 2) EXTRACELLULAR (blood plasma of mammals):

bicarbonate buffer system (CO2 + H2O <--> H2CO3 <--> H+ + HCO3–)

3 linked equilibria:



How can the [HCO3–] / [H2CO3] system effectively buffer the blood plasma at pH ~7.4, with a pKa

well below 7?

clinical considerations of bicarbonate buffer system:What happens physiologically if the blood pH↓ (i.e. [H+]↑ (acidosis)You exhale excess CO2, so [CO2]↓, so (Le Chatelier's Principle)

[H+]↓, i.e. pH goes back up.What happens physiologically if the blood pH↑ (i.e. [H+]↓ (alkalosis)You exhale less CO2, so [CO2]↑, so (Le Chatelier's Principle)

[H+]↑, i.e. pH goes back down. What if you have difficulty exhaling (respiratory failure)?Blood [CO2]↑, so [H+]↑ (acidosis) and you can't get rid of the excess [CO2] by exhaling.

Treatment: inject bicarbonate (HCO3–) to convert some of the excess H+ to H2CO3, which

would bring pH back up -- and get the person breathing again to get rid of the excess CO2!

[email protected] .eduDepartment of Biochemistry & Molecular Biophysics

The University of ArizonaCopyright (©) 2007All rights reserved.

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Lecture 1: Introduction, Noncovalent Interactions, and ...cbc.chem.arizona.edu/.../spring/460web/lectures/LEC1_Intro_Water.pdf · biological milieu is primarily aqueous -- water is