BCHM 3050 : Chapter 2 - Weak Interactions in an Aqueous Environment

The type of non-covalent interaction that involves *pie bond stacking*

Dispersion (van der Waals)

Why does DNA carry a negative charge at a neutral pH?

Due to the large numbers of phosphate ions used for the backbone of DNA

The type of non-covalent interaction that has a donor and acceptor half and who's *bond length is fixed* (can't get closer together)

Hydrogen Bond

Although Hydrogen bonds are supposed to be at fixed lengths, Increases in atomic radii lead to increases in _____________ distances

Hydrogen-bonding (H-bond)

Water Density

Ice has a lower density than the liquid form of water -Density is greater in liquid

Amphipathic Compounds can form what types of substances?

Monolayer Micelle Bilayer EX: lipids and fatty acids, polarized heads and long stringy tails (phospholipid bilayer)

List the following energies of Noncovalent Interactions in biomolecules from the most energy to the least - van der Waals - charge - charge - Hydrogen bonds

Most = charge-charge Med= Hydrogen bonds Least = van der Waals/dispersion

what are the elements that can hydrogen bond?

N, O, or F

What is the main difference between noncovalent and covalent bonding?

Noncovalent bonds are not to be confused with chemical bonds (i.e. covalent), which are the forces within a molecule that holds atoms together.

Examples of INDUCED dipoles

Stacked rings

Solubility

The quantifiable property that measures how much of a solute will dissolve in a solvent (g/100 mL)

T/F: the presence of polar covalent bonds does not guarantee you will have a polar molecule, *molecular symmetry* plays a role!

True

Examples of PERMANENT dipoles

Water (H2O) Carbon Monoxide (CO)

What holds the strands of DNA together so they won't repulse away from each other due to their like charges?

a protein with overall positive surface charge

Difference between an acid and/or base

a single proton

Noncovalent bonds a) what is it a result of? b) what is another term for these formation of bonds between 2 or more molecules?

a) "equal" sharing of electrons in a covalent bond; attraction of ions of different charges b) intermolecular forces

Covalent bonds a) what is it a result from? b) what are the typical atoms involved? c) what periodic trend plays a huge role?

a) "unequal" sharing of electrons b) nonmetals c) electronegativity

Dielectric Constant a) what does it represent and or measure? b) the constant can be envisioned as what? c) the higher the dielectric constant, what is the effect on charged species?

a) *The screening effect of a medium is represented*; charges are screened in solution by the medium that exists between the charges. *A quantity measuring the ability of a substance to store electrical energy in an electric field.* b) insulation c) lesser the attractive force between charged species .

Arrhenius Acids a) define b) what do they form if dissolved in water?

a) Compounds that form H3O+ if they dissolve in water. b) OH- ions

Clathrate structures a) how do they form? b) if you order water in this form of structure what occurs to the overall entropy? c) Is this change in entropy favorable? d) this particular phenomena is associated with _______________________ molecules

a) Concerning non-polar molecules, *a polar solvent (i.e. water) can form "clathrate" structures that surround (or trap) nonpolar surface areas or molecules* b) decreases entropy of overall water solvent c) a decrease in entropy is considered unfavorable. d) hydrophobic

Hydrogen bonds site a) the donor site will always have _________________________ b) The acceptor will be either __________________ and between it is where a _______________________ will form

a) H covalently bonded b) N, O or F; hydrogen bond

Mastering Question Much is made of water's ability to dissolve a wide variety of molecules and yet, one of its most important characteristics is its effect on nonpolar, uncharged molecules. Which of the following statements is NOT true about this effect? a) Hydrophobic molecules are driven together largely because of forces of attraction between them. b) The hydrophobic effect plays an important role in the folding of proteins and the assembly of lipid bilayers. c) Water molecules form clathrates or cages that surround nonpolar molecules or particles. d) All of the listed statements are true.

a) Hydrophobic molecules are driven together largely because of forces of attraction between them. Reason: it's wrong since hydrophobic means water opposing molecules--> there's no attractive forces

Salt bridge a) define b) the salt bridge is governed by what law?

a) The simplest electrostatic interactions are those between a pair of oppositely charged particles b) Coulomb's Law

Which set of compounds would form a buffer in aqueous solution? a) HF and KCN b) HCl and KCl c) NaCl and KCl d) NaBr and KBr e) HCOOH and HCOONa f) HF and NaF g) KF and KOH

a) conjugate base of HF will be KF and not KCN So, they will not form buffer b) HCl is strong acid. So, they will not form buffer. c) NaCl and KCl are both salt. So, they will not form buffer. d) NaBr and KBr are both salts. So, they will not form buffer e) HCOOH is weak acid and HCOONa is its conjugate base So, they will form buffer f)HF is weak acid and NaF is its conjugate base So, they will form buffer g)KOH is strong base here So, they will form buffer

Hydrophilic vs. Hydrophobic a) The preference of a molecule for or against water often plays a role in determining its ________________ in a aqueous environment (ie: cells are an aqueous environment) b) Many molecules are attracted to water due to various intermolecular forces; such molecules are termed _____________________ c) Molecules that are repelled from water due to their forces are termed as _________________________

a) function b) hydrophilic c) hydrophobic

a) Describe how MP/BP/Vap increases in various compounds b) label the following from highest to lowest based on their MP/BP/Vap properties : CH4, NH3, H2O, H2S

a) increases with an increase in size and/or EN b) Highest to Lowest: H2O NH3 H2S CH4

Water as a solvent a) why is it known as the "universal solvent" b) what properties gives it it's great solvent abilities?

a) it is able to dissolve more substances than any other liquid. b) its ability to form a number of intermolecular forces with other molecules.

Water being amphoteric and amphiprotic molecule a) what does it mean when water is termed as being "amphoteric" b) what does it mean when water is termed as being "amphiprotic"? c) why do these 2 terms although similar not mean the same thing?

a) it is able to react as either an acid or a base? b) it is capable of donating or accepting a proton (H+). c) The species Al2O3 is also amphoteric...but not amphiprotic b/c it does not contain a proton!

pH scale a) The pH scale is based on a _________________ scale approach b) Most biological reactions take place between pH range of? c) the pH of human blood is around d) the physiological pH commonly used is __________ e) any deviations from the human pH levels can lead to

a) logarithmic pH = -log (H) b) 6.5-8.0 c) 7.35-7.45 d) 7.4 e) health problems

Hydrophobic Effect a) which molecules and/or compounds does this effect take place with? b) what function does it allow for? c) what does it prevent and how? d) T/F: the solvent entropy is higher e) what does the folding of proteins do to entropic values?

a) macromolecules and proteins b) stabilize structures by driving non-polar side chains together during folding. c) *prevents clathrate type structures*; limiting interaction between hydrophobic groups and the water molecules d) true e) decreases them, but it is still a favored process

Isoelectric Point (pI) a) define b) At lower values of pH proteins will carry more ________________ charge c) At higher values of pH proteins will carry a more _________________ charge d) label the formula

a) pH where a molecule or compound is electrically neutral; the average charge on the molecule is 0. -Add ALL charges together = 0 b) positive c) negative

Dissolution a) define the process b) How is the favorability of this process determined c) it is a property of ________________________ molecules in aqueous solution

a) process of mixing solvent (i.e. water) and solute (i.e. proteins) b) by the *type and bond energies of the intra- and intermolecular forces* present between the solvent and solute. c) Hydrophilic

Buffer Solutions a) define buffers b) effect on buffers to a pH value of +/- 3 pH units from pKa c) effect when pH=pKa

a) resist any changes in pH following the addition of acid or base within +/- 1 pH unit of the pKa solution. b) group is essentially fully deprotonated or fully protonated, and the buffer effect ceases. c) the group is 50% protonated/deprotonated, thus it is 50% ionized.

Coulomb's Law a) what is the relationship? b) Under what condition does this law apply?

a) the force of attraction between 2 point charges gets weaker the farther the distances of the charges. b) only in a vacuum

Henderson-Hasselbalch equation a) what is used for? b) label the formula c) pKa > pH... what's favored? d) pKa < pH

a) used to calculate the average charge (ionization) on an ionizable group at any pH: "[base]/[acid]" b) *pH = pKa + log [A-]/[HA]* c) acid d) base

pH scale is based on the

auto-ionization of water

The unequal sharing of electrons within a water molecule makes the water molecule _____. a) hydrophobic b) polar c) have a low surface tension d) ionic e) change easily from a liquid to gaseous form

b) polar Reason: The electrons spend more time with the oxygen of the water molecule than with the hydrogens of water. Thus, the oxygen has a net negative charge and the hydrogens have a net positive charge.

A _________________ is required to fully solubilize a given protein

buffer (with set ionic strength)

Which bonds are the weakest? a) Ionic bonds b) covalent bonds c) hydrogen bonds

c) hydrogen bonds Reason: Hydrogen Bonds are weaker than covalent bonds because they do not involve sharing of electrons, and they are weaker than ionic bonds because they involve the attraction of partial (not full) opposite charges.

Amphipathic Compounds

contain hydrophilic and hydrophobic groups

Mastering Question Each water molecule is joined to ________ other water molecules by _____________ bonds. a) two ... hydrogen b) three ... ionic c) four ... polar covalent d) four ... hydrogen e) two ... polar covalent

d) 4, hydrogen

Mastering Question Which of the following statements about noncovalent bonding interactions is NOT true? a) All noncovalent bond interactions are inherently electrostatic in nature. b) Van der Waals interactions, also known as dispersion forces, are the weakest of the attractive noncovalent bonding interactions. c) A charge may induce formation of a dipole in a nearby polarizable molecule. d) Charge-induced dipole interactions are inversely proportional to the square of the distance between the two atoms.

d) Charge-induced dipole interactions are inversely proportional to the square of the distance between the two atoms. The reason it's incorrect: charged-induced dipoles are directly proportional to the square of the distance between the 2 atoms.

Which of the following is FALSE when considering van der Waals interactions? a) Van der Waals radii can determine molecular surfaces. b) Molecules that interact by van der Waals forces do not interpenetrate. c) The total interaction energy is the sum of the attractive and repulsive forces. d) They are not important in determining the stability of three-dimensional structures of proteins.

d) They are not important in determining the stability of three-dimensional structures of proteins.

Mastering Question Noncovalent bonds are critically important to the function of biomolecules. Which of the following is/are (a) valid reason(s) for this importance? a) The effect of these weak interactions is cumulative. b) Their bond energies are ~10-100 times weaker than ordinary covalent bonds. c) Noncovalent interactions are made up of hydrogen bonding, electrostatic interactions, and dispersion forces. d) All of the listed statements are valid reasons for this importance.

d) all statements are true

What is the predominant intermolecular force in the liquid state of each of these compounds: methanol (CH3OH), carbon tetrachloride (CCl4), and methyl chloride (CH3Cl)? label based on the premise of the following: dipole-dipole dispersion hydrogen bonding

dipole-dipole: CH3Cl hydrogen: CH3OH dispersion/ london forces: CCl4

Mastering Question Each of the following is a noncovalent interaction EXCEPT: a) the interaction between an amino and a carboxylate group. b) a hydrogen bond. c) an interaction between NH3+ and a water molecule. d) a van der Waals interaction. e) a carbon-hydrogen bond.

e) a carbon-hydrogen bond Why not: A non-covalent interaction does not involve the sharing of electrons, but involves the dispersed variations of electromagenetic interactions between or within a molecule. Carbon hydrogen bond is a covalent bond as it is made by sharing of the electrons by each atom. The electronegativity difference between C and H is less hence a covalent bond is formed by sharing of electrons.

All noncovalent interactions are _____________________ in nature

electrostatic

what effects the energies between atoms or molecules?

environment

Water has a __________ heat capacity and dielectric constant (~80 F/m)

high

Water likes to remain as a ____________________ at room temperature

liquid

The structure of water is said to be a _______________________

molecular lattice

Acids and bases are essentially________________

opposites

Formula for indicating pKa

pKa = -log (Ka)

Water is a _____________ dipole, due to its shape/structure and unsymmetrical (104.5 bonds)

permanent

Charge seperation a) what gives rise to this event?

permanent and induced dipoles

What is the main purpose of H-bonding of biomolecules

stabilizes the structural elements

A lower pKa indicates...

stronger acid

Noncovalent interactions are important in helping define what?

structure and function of biomolecules

auto-ionization of water

the ability of one water molecule being able to donate a proton to a second molecule of water

What is the main purpose of the amphipathic compounds forming all of the various substances and layers that it does?

they help form these structures in order to help increase the entropy or to prevent the formation of clathrate *remember that a decrease in entropy during the hydrophobic effect is unfavorable*

t/f: Bases need not contain -OH directly; instead, they can increase the concentration of -OH by deprotonating water.

true

what is an acid buffer composed of?

weak acid and salt of weak acid

what is a basic buffer composed of?

weak base and salt of weak base

Mastering Question Which statements about hydrogen bonds are correct? 1) Hydrogen bonds are the interaction between a hydrogen atom bonded to an electronegative element and the lone pair of electrons on a nearby electronegative atom. 2) The atom to which the hydrogen atom is covalently bonded is the hydrogen-bond donor. 3) The distance between the covalently bound H atom and its hydrogen-bonding donor is the sum of its van der Waals radii. 4) Hydrogen bonds can be stronger interactions than even charge-charge interactions.

1, 2, 4 3 is incorrect: *The distance between covalently bonded H atom and its hydrogen bonding donor is shorter than Van der Waals radii*. Hence, the above statement is incorrect.

How many Hydrogen donor and acceptor sites in water?

2 H-bond donor sites 2 H-bond acceptor sites

Mastering Question Which statements regarding the Henderson-Hasselbalch equation are true? 1) If the pH of the solution is known as is the pKa for the acid, the ratio of conjugate base to acid can be determined. 2) At pH = pK a for an acid, there is an equal amount of conjugate base to acid in solution. 3) At pH >> pK a for an acid, the acid will be mostly ionized. 4) At pH << pK a for an acid, the acid will be mostly ionized.

4) At pH << pK a for an acid, the acid will be mostly ionized. reason it's false: if pH<<pKa , then log ((conj. base) / base )<0 therfore: conj. base < acid

what are buffers composed of?

A buffer contains significant amounts of a *weak acid and a salt containing its conjugate base.* The acid consumes any added base, and the base consumes any added acid. In this way, a buffer resists pH change. *Strong acids, strong bases, two bases, or two acids cannot form a buffer on their own.*

Which statements about lipid bilayers are true? 1) Their formation is driven by the hydrophobic effect. 2) The amphipathic molecules that make up the bilayers orient themselves such that their polar head groups point out toward the aqueous solvent and their hydrophobic tails are pointed toward the interior of the bilayer. 3) They serve the role of physical compartmentaliza tion of components within a cell. 4) They are made primarily from phospholipids.

All are true

Where will the protein have the lowest degree of solubility?

At the PI -Surface charge = 0

Bronsted- Lowry bases

Compounds that accept protons

Lewis Acids

Compounds that can accept electrons

Lewis bases

Compounds that can donate electrons

Bronsted-Lowry Acids

Compounds that donate protons (H+)

Which bonds have a higher energy, IMF (intermolecular forces) or covalent bonds?

Covalent