Chapter 2

pH formula

pH = -log[H+]

sign of force (F) if q1 and q2 same sign

F is (+)--means repulsion

bases

H+ (proton) acceptors

[H+] and [OH-] of pure water

H+ and OH- equal so [H+]=[OH-]=1 x 10^-7--this is neutral solution at 25C -human body is 37C so [H+]=1.6 x 10^-7

energy of H bonds compared to other noncovalent bonds

relatively high

viscosity

resistance to flow

electronegativity

tendency to pull electrons toward itself

dielectric constant of water vs. other liquids

-high const for water -lower for organic liquids

hydrophobic effect

-hydrophobic nonpolar surfaces aggregate -surrounding 2 hydrophobic molec w/ 2 separate cages requires more ordering of water cages than surrounding both molecules w/ a single cage -hydrophobic moleucles aggregate to release some ordered H2O molec from the clathrates to increase entropy of solvent--enables released H2O to form more H-bonds w/ bulk H2O--increases entropy -ex) folding protein moleucles, self-assembly of lipid bilayers -see last pic

strong base

-ionizes entirely, releasing OH- ion (powerful proton acceptor) -ex) NaOH

heat capacity of water

-large, so water can act like temperature buffer and maintain body temp -ex) prespiration to transfer heat to skin to environment

Coulomb's law (formula)

-measures force between a pair of charged ions in a vaccuum -given ions: q1 and q2 -distance=r -k=constant (value depends on the units being used) -Force= (F)

dipole interactions

-molec w/ no net charge can have asymetric internal distribution of charge -electron distribution of the uncharged carbon monoxide molecule: oxygen slightly more negative than carbon end--*polar* *(has dipole moment (μ))* -dipole moment shows magnitude of a molecule's polarity. -In molecules with a more complex shape (water) the dipole moment is the vector sum of the dipole moments along each polar bond -in water, electrons are drawn away from hydrogens towards the oxygen atom b/c of greater electronegativity -molecules w/ large dipole moments are said to be highly polar -includes: 1. dipole-dipole interactions 2. charge-dipole interactions -Unlike simple charge-charge interactions, the energies of dipole interactions depend on the relative orientation of the dipoles and they are of shorter-range interactions -energy of a charge-dipole interaction is proportional to 1/r^2 -energy of a dipole-dipole interaction is proportional to 1/r^3

what angle is most stable for H-bonds (angle when hydrogen bonds are strongest)?

-most stable H-bonds are at 180 degrees (angle between donor, the shared H atom, and the acceptor--the 3 atoms are colinear) -in water and DNA double helix

hydrophobic molecules

-non-polar, non-ionic substances don't have good interaction w/ water -don't form H-bonds w/ water and don't form hydration shells--energetically favorable interactions -water forms *clathrate structures* "cages" around non-polar molecules--energetically unfavorable b/c water molecules are ordered (decreases entropy)

table of weak acids and their conjugate bases

-note: some weak bases don't necessarily have OH groups but they increase OH conc of soln by extracting proton from water -the stronger the acid, the weaker its conjugate base (conj base accepts a proton less to reform acid)--strength of acid (tendency to donate protons) idicated by Ka and pKa)

best buffering capability *(what does the pH equal to in midpoint of titration?)*

-pH of solution changes very little with each increment of acid or base added, when close to pKa of a molecule. -This is b/c conjugate acid or bases are present in sufficient amount to combine with added H+ or -OH to neutralize them -pic: shows titration curve that measures pH against moles of base added per mole of acid originally present--note: over much of titration curve, pH lies withing one pH unit below or above pKa *-at the midpoint of the titration where half the acid is neutralized, pH=pKa*

table of non-polar interactions

-pic: The symbols delta negative or delta positive indicate partial electron or proton charge--seen in molecules that share electrons unequally

how can uncharged, yet polar molecules dissolve in water?

-polar molecules (proteins, nucleic acids w/ polar groups) can form H-bonds w/ water molecules -these are hydrophilic molecules -ex) molecules w/ internal H-bonds like helix dissolve in water b/c some of their internal H-bonds may be in dynamic exchange for H-bonds to water

ex) Ca2+ ion and Cl- ion are separated in soln by 6Å. Will energy of interaction btw ions be greater when intervening medium is water (ε=80.1) or ethanol (ε=24.5)?

-put in equation and value larger for ethanol so ethanol

dielectric constant of water

-results from polar nature of water molecule -electric field generated btw 2 dissolved ions causes extensive orientation of intervening water dipoles--oriented dipoles contribute to a counterfiled, reducing the effective electrostatic force btw the two ions

michelles

-spherical structure formed by a single layer of molecules -hydrocarbon tailes of molecules parallel to each other and interact via van der Waals interactions

human growth hormone (hGH) and muscle tissue growth (Example of chemical interactions that result in a biological phenomena)

-stimulation of muscle tissue growth in response to human growth hormone results from forming weak (but highly specifc) bonding interactions between the hGH molecule and growth hormone receptor on surface of muscle cell -The binding of hGH to its receptor transmits a signal across cell membrane--provides signal for cell growth. -The interaction between hGH and its receptor is result of specific noncovalent bonding interactions.

conc of H+ in high and lower pH

higher pH=lower [H+] lower pH=higher [H+]

what else are noncovalent interactions important for?

inter-molecular interactions (like prev example) -these bonds not as strong as covalent interactions so molecules can interact in non-permanent way

surface tension

the resistance of a liquid surface to distortion or penetration

equilibrium acid dissociation constant

-*acids w/ larger Ka dissociate more readily*

how many times weaker are non-covalent bonds than covalent bonds?

-10-100x -weakness lets them be continually broken and re-formed

amphiphatic molecules in solution

-Amphipathic molecules have both hydrophobic and hydrophilic properties. (ie. fatty acids, lipids, detergents) -Polar head can interact with water. -Nonpolar components tends to hide from water. -ex) phospholipids in membranes -ex) proteins often have portions that are hydrophobic and hydrophilic--Allows them to interact with a membrane and the aqueous environment.

charge-induced dipole interaction

-An anion or cation induces a dipole in a polarizable molecule and then is attracted to it

polarizability of aromatic rings

-Aromatic rings are very polarizable because the electrons can easily be displaced in the plane of the ring -ex) Benzene rings are polarizable: electrons can be displaced within the ring

How does the pH of a solution affect the charge on a molecule w/ multiple ionizable groups? (amino acid glycine)

-At low pH, below both pKa values, the species is fully protonated and overall charge is +1 -As pH increases, the group with the lower pKa (2.3) is deprotonated. -If pH increases further and goes above next pKa value (9.6), both groups become deprotonated. -The overall charge is now -1

ion product of water

-B/c Kw is a constant, if change [H+] of [OH-] by adding acidic/basic substances to water, the other conc must also change

blood buffering system

-Blood uses a carbonic acid-bicarbonate system with a pKa ~ 6.3 to keep blood pH in acceptable range.

H-bonding between H2O molecules in ice

-Each water molecule can make up to 4 hydrogen bonds. -Each molecule is a donor and an acceptor -H-bonding btw water molecules most regular when water freezes--creates a rigid tetrahedral molecular lattice--each molecule bonded to 4 others (fewer H-bonds in water than ice) -H-bonds leave more space between molecules and makes it less dense

van der Waals interactions (dispersion forces)

-Even two molecules that have neither a net charge nor a permanent dipole moment (nonpolar) can attract each other if they are close enough. -The distribution of electronic charge in molecules is never static, but fluctuates. -When two molecules approach very closely, their charge fluctuations tend to localize an area of partial positive charge on one molecule next to an area of partial negative charge on the neighbor, producing a net attractive force -vander Waals attractive energy works at very short range (1/r^6) -van der Waals interactions are individually weak, but collectively stable -but when 2 molecules come too close, their electron orbitals overlap, and there is mutual repulsion -Their repulsion increases very rapidly as the distance between their centers (r) decreases -the energy of attraction increases as the atoms become closer and closer together until the point at which their electron orbitals begin to overlap and they begin to repeal each other. -The highest energy of interaction occurs when the energy of interaction is most negative at the optimal *van der Waals contact distance*, the most effective radius for close molecular packing--Closer than contact distance leads to repulsion -2-4kJ/mol

acids

-H+ (proton) donors

surface tension of water

-H-bonds make it have high surface tension

induced dipole interactions

-Molecules that don't have permanent dipole moments can become polar in presence of an electric field or charge, produced by a neighboring charged or polar molecule -Interactions of *polarizable* molecules are called induced dipole interactions. -includes: 1. charge-induced dipole interaction 2. dipole-induced dipole interaction -These have even shorter range of interactions than permanent dipole interactions. -energies of induced dipole interaction proportional to 1/r^4 -energies of permanent dipole interaction proportional to 1/r^5

dissociation of strong acids vs. weak acids

-Strong acids lose their hydrogen protons, dissociate, more completely than weak acids.

pKa

-The acid dissociate constant (Ka) is often expressed as pKa (the negative log of both sides of the equation) *pKa= -logKa* -larger Ka=smaller pKa -larger pKa ,eams weaker acid and smaller pKa means stronger acid -The pKa is the pH at which the acid is 50% dissociated. -Based on Henderson-Hasselbalch equation: -As the pH increases, more -OH present, an acid will become more dissociated. -As pH decreases, more H+ present, acids and bases become protonated.

hydrogen bonding

-The interaction of a Hydrogen (covalently bound to another atom) with a pair of nonbonded electrons on another atom (typically O or N) -Sometimes H doesn't share electrons equally in a covalent bond, when bonded to an electronegative atom, hydrogen develops slight positive charge and interacts with a pair of e- from a diff atom -H-bond donor=atom to which the hydrogen is covalently bonded -H-bond acceptor=atom w/ the nonbonded electron pair -H-bonds have both covalent and noncovalent features.

stability and flexibility of non-covalent interactions

-Within a single molecule multiple noncovalent interactions add up to form bond energies up to several hundred kJ, allowing a structure to form a stable, yet flexible, 3D structure--can be important to its function

dipole-induced dipole interaction

-a permanent dipole induces a dipole in a polarizable molecule and then is attracted to it

how pH of a solution changes the overall charge on a molecule (how does pH affect protein charge?)

-as pH changes, so does the degree of protonation or deprotonation of acidic or basic groups on amino acids, depending on their pKa--can change overall charge of molecule -pic: proteins will caryy more positive charge at lower values of pH -that's why need to keep body at specific pH

ex) given: ionic radii of Ca2+, K+, and Cl- are respectively 1.14Å, 1.52Å, and 1.67Å. Are the ionic bonds stronger in a crystal of KCl of Ca Cl2?

-assume ε=1 -k is constant so ignore -use formula -charge on K+ is +1, Ca2+ is +2 and Cl- is -1 -do q1 x q2 for each and CaCl2 is larger -need to find radii, so r=1.52Å+1.67Å=3.19Å for KCl r= 1.14Å+1.67Å=2.81Å for CaCl2 -so charge bigger and radius smaller for CaCl2 and CaCl2 crystal has stronger ionic bond

melting/boiling point of water

-b/c of hydrogen bonds, water has high melting and boiling point compared to other hydrogen compounds--b/c water can form so many H bonds -heat of vaoprization is high (energy needed to boil one mol of water)

charge-charge interactions in a biological environment (Coulomb's law in biological system formula) (*energy of interaction*)

-biological environ not a vacuum b/c in cell, charges surrounded by water/other molecules--screens the charges from one another so actual force btw 2 charges always less than what was given for previous equation -screening effect expressed by including the dielectric constant (ε)--the higher the dielectric constant, the weaker the force between the separated charges -Coulomb's law is an expression of Force; but, every bond formation or cleavage process involves a change in energy. -Changes in energy drive all biochemical processes, thus when we consider changes in noncovalent bonding interactions, we are interested in the *energy of interaction (E)*--formula

formula for dissociation of weak acid

-can be any one of these -note: sometimes conjugate base has a negative charge, but in ALL cases, it has one fewer proton than acid -middle one is most generic form

what interactions stabilize a salt crystal

-charge-charge interactions stabilize a salt crystal

what gives the complex structures of biological molecules?

-covalent bonds hold atoms together (linear sequence of DNA), but complex structures made by weaker, noncovalent interactions that allow large macromolecule to fold and make 3D structures (double helix of DNA)

weak acids and bases

-dissociate partially -in an aqueous soln of weak acid, there is an equilibrium between acid and its conjugate base -note: conj base is the substance that can accept a proton to re-form the acid

strong acid

-dissociates almost completely into a proton and a weak conjugate base -ex) HCl-->H+ + Cl- (the H+ conc in solution is almost equal to the molar conc of HCl added)

reason for covalent and non-covalent feature

-distance between H and O in a hydrogen bond between them is 1.9Å, but sum of their van der Waals radii is 2.9Å. -a covalent H-O bond length is 1.0Å, but distance between hydrogen-bond donor and acceptor is 2.9Å

Charge-Charge Interactions (Ionic Bonds, salt bridges)

-electrostatic interaction btw a pair of ions formed when one atom loses an electron to another atom--atoms will carry a net charge b/c have diff # of protons and electrons -will have attractive interaction based on opposite charges -When an atom has only 1 or 2 e- in the outer shell, It donates to another atom

what do noncovalent interactions depend on?

-electrostatic nature--depend on the forces that electrical charges exert on one another

heat capacity

-energy needed to raise/lower the temp of a substance by 1 degree C

energy of interaction

-energy required to separate 2 charged particles from a distance of r to infinite distance -energy of an oppositely charged pair, q1 and q2, is always negative, but E approaches zero as r becomes very large -it is also affected by the value of the dielectric constant, in that ionic bonds come apart in the presence of water because it has a relatively high dielectric constant--This leaves free ions, called electrolytes, as dissolved substances in our body. -ex) Charge-charge interactions are often responsible for specificity of interactions between proteins and binding targets (Ab—antigen)

van der Waals as a team

-stronger if have more that work together -real molec not spherical and have complex shapes -pic: complex molecules in a "space-filling" manner, which represents each atom by a sphere with its appropriate van der Waals radii (right pic) -Van der Waals interactions strong when two molecules pack tightly together with each other--Each interaction is weak its own, but collectively can make significant contributions to the stability of biomolecules. -Protein-protein Interactions (interaction energy increases with total contact surface area)

H-bonding between H2O molecules in water

-structure of liquid water described as "flickering clusters" of H-bonds (remnants of ice lattice continually breaking and re-forming as molecules move about -liquid water more dense than solid b/c when lattice breaks, molecules move closer together -more dense liquid state is favored over less dense solid state (even at high pressures)

what happens when you shake amphipathic liquids in aquaeous solns? how do membarnes form?

-they can form micelles, spherical structures, or bilayer vesicles -monolayer can form on water surface (only head groups immersed) -The amphipathic nature of polar lipids is how membranes are formed.

number of H bonds a water molecule can make

-two pairs of unbonded electrons on oxygen can by H-bond acceptors -OH groups can be H-bond donors -so each molecule can make 4 H bonds

structure of water

-unpaired electrons are good H-bond acceptors

variation in the dependence of bond energy on distance

-variation in the dependence of bond energy on distance predicts that charge-charge interactions are stronger over much longer distances than are van der Walls interactions -the bond energy of charge-charge interactions is significantly stronger than van der Walls interactions

ionization of water

-water can ionize and acts a weak acid/base -one water molec can transfer a proton to another to yield a hydronium ion (H3O+) and a hydroxide ion (OH-)

viscosity of water

-water has high viscosity--caused by H-bonds

water as a solvent

-water is a polar solvent (dissolves ionic molecules) -negative end of the dipole can interact with cations and the positive end can interact with anions -Energy required to dissociate two atoms

The tendency of ionic compounds to dissolve in water is because... (2 things)

1) formation of hydration shells energetically replaces the ionic interaction--ions become *hydrated*--surrounded by shells of oriented water molecules called *hydration shells*--formation of hydration shells is *energetically favorable*--energy released in these favorable hydration interactions compensates for the loss of charge-charge interactions stabilizing the crystal 2) the dielectric constant of water decreases the force between oppositely charged ions that would pull them back together.

6 polar molecules

1. hydroxyl group 2. carbonyl group 3. ester group 4. ammonium group 5. carbozylate group 6. phosphate monoester

which atoms are sufficiently electronegative to serve as strong donors in biological compounds?

1. oxygen 2. nitrogen -these are the only ones -C-H groups don't form strong hydrogen bonds, but O-H groups do

bond energies of C-C and C-H covalent bonds

150-400 kJ/mol

physiological pH range

6.5-8.0

pH of living cell

7.2-7.4 (except stomach and lysosomes) -Control of physiological pH is tightly controlled by buffers in the body.

polarizable

A molecule in which a dipole can be induced is said to be polarizable

covalent feature of H bonds

Electrons are shared between acceptors and donors

sign of force (F) if q1 is (+) and q2 is (-), or vice versa

F is (+)--means attraction

charge-dipole interaction

In the aqueous environment of the cell, a polar molecule can be attracted by a nearby ion

dipole-dipole interaction

In the aqueous environment of the cell, a polar molecule can be attracted by another polar molecule

noncovalent feature of H bonds

There is also a charge-charge interaction between the partially-pos. H and the partially-neg. acceptor (non-covalent)

Hasselbalch equation

[A-] is deprotonated form; [HA] is protonated form