Water, Molecular Interactions, and Acid-Base Chemistry

What is soluble in charged water?

Most intermediates of metabolism ex: nucleic acids and proteins

How do lipid bilayers form?

Spontaneously in water and are stabilized by their interaction with water

Describe ionization behavior

Water can dissociate and because of that it can conduct electricity

Describe a buffer

Is made of a weak acid and a salt. It can also resist changes in pH

When do enzymes in a cell function optimally?

At a near neutral physiological pH

Properties of water

-highest melting point, boiling point, and heat of vaporization compared to any natural/biological liquid

What is the structure of water and what causes it to have these unique properties?

Water H2O has 2 lone pair electrons that are available to interact with others. The hydrogen interacts with the oxygen via hydrogen bonds which are longer and weaker than covalent bonds. Water is in a tetrahedral arrangement. It also has a dipolar nature with H being slightly positive and O being slightly negative which allows it to have unique properties

Why is water called a flickering structure

Because it is loosely connected to itself via hydrogen bonds. The molecular structure of ice doesn’t “flicker” as it is more structurally sound as opposed to the fluid liquid state

Regarding the thermodynamics of water how do ice, and liquid water relate?

Both will melt or evaporate at room temperature. Causing a spontaneous reaction. This means that Delta G is negative and Delta H is positive, so entropy must increase making it the driving force of this reaction

What are H-bond acceptors what are some examples?

Acceptors: must have an available electron OR have the opportunity to create a dipole in the molecule (N-H, O-H)

When are hydrogen bonds strongest?

When it is bonded in a straight line (direction matters)

Why won’t thymine interact with Guanine or cytosine?

Not only because they are structurally different but they cannot form the appropriate hydrogen bonds

What are the 5 different types of non-covalent bonds?

Hydrophobic interactions

Pi stacking

Van der Waals

Hydrogen bonds

Electrostatic( this and bonus are very strong)

Bonus: salt bridge(combo of hydrogen bonds and electrostatic)

Why are non-covalent bonds important

Allow for more dynamic movement of molecule as opposed to to the rigid firm covalent bond.

What is an Amphipathic molecule?

A molecule with both hydrophobic (nonpolar)and hydrophilic (polar/charged)tendencies

Describe a long chain fatty acid

They have a hydrophilic head with a hydrophobic alkyl group (amphipathic) which makes organized “cages” of water surround the -phobic group

Is a lipid polar or non polar and will it dissolve in water?

Non polar and no.

Walk through how amphipathic molecules interact in water and how Micelles are formed.

When lipids are in water it forces water to make a cage around them, as the lipids start to move closer together they interact removing part of the cage and forming a lipid bilayer this also has a positive entropy effect. As more lipids come together micelles are formed further increasing the entropy

How are macromolecules stabilized?

Through maximizing weak interactions- water tightly bound to biomolecules

How is water partially ionized?

Via reversible ionization thus allows water to form a proton and hydroxide which can either rehydrate itself to share the proton with a different molecule.

Why are water molecules prone to “proton hopping” ?

Because of waters electrical conductivity which slows us to further determine dissociation

How is the equilibrium constant found?

Concentration of products multiplied together all divided by the reactants

How is the ionization of water found? And what is it?

Kw-ion product of water

Keq- equilibrium constant of water=1.8×10^-16M

Kw=Keq[H2O]=[H][OH]=1.0×10^-14M²

How to find and what is the neutral pH?

Set [H]=[OH]=the square root of Kw-ion product of water

=1×10^-7M

What is the concentration of OH- in a solution with an H+

concentration of 1.3x10-4 M?

Begin with the equation for the ion water product.

Kw = [H+][OH-] = 1.0 x 10-14 M2/ 1.3x10-4 M=7.7×10-11M

What is the pH expression

pH=log(1/[H+])=-log[H+]

What is the pH scale based off?

The pH scale is based on the ion product of water, Kw

Describe pH values > 7

alkaline or basic,

concentration of OH– is greater

than that of H+

Describe pH values < 7

acidic, concentration of H+ is greater than that of OH

What is Bronsted-Lowry Acid?

It donates protons and forms a conjugate base that is a proton acceptor

Acid dissociation equilibrium constant

K= ([H3O+][A+])/([HA][H2O])

What is the water concentration in a dilute aqueous solution?

Essentially constant

Explain strong and weak acid and bases as it pertains to Bronsted Lowry theory

Strong acid or bases are completely ionized in aqueous solutions while weak acids and bases can act as a buffer.

Acid dissociation constant

Ka=K[H2O]=([H+][A-])/([HA])

pKa formula

=log(1/Ka)=-logKa

What is the Henderson-Hasselbalch Equation

pH=pKa+log([A-])/([HA])

What are the uses does the H-H equation

• Calculate pK a, given pH and the molar ratio of H+ donor and acceptor

• Calculate pH, given the pK a and the molar ratio of H+ donor and acceptor

• Calculate the molar ratio of H+ donor and acceptor, given the pH and pK a

• With these molar ratios, calculate the net charge of a molecule in solution

describe optimum pH

the characteristic pH at which enzymes typically show maximum catalytic activity

What is Pepsin

is a digestive enzyme secreted into gastric juice, which has a pH of ~1.5, allowing pepsin to act optimally.

What is Trypsin

is a digestive enzyme that acts in the small intestine, and has a pH optimum that matches the neutral pH in the lumen of the small intestine.

Alkaline phosphatase

of bone tissue is a hydrolytic enzyme thought to aid in bone mineralization.