Biochem Exam 1 Unit 2

Brownian motion

Water and gas molecules of the environment bounce randomly at a rate determined only by the temperature (thermal motion). When these molecules collide with larger structures like pollen granules or large biomolecules, they cause the particles to move randomly too.

What are the properties of water that make it the perfect environment for life?

• water renders molecules mobile and permits thermal-motion powered interactions between molecules

• Polarity allows hydrogen bonds

• cohesive- hydrogen bonded clusters of molecules are continually forming and breaking apart

• Can dissolve many molecules- doesn’t dissolve others

• Hydrophobic effect/interactions

List three of the fundamental noncovalent interactions in biochemistry

Ionic interactions- interactions between distinct electrical charges on atoms, energy of electrostatic interaction between 2 ions is given by Coulomb force equation

van der waals- depends on transient asymmetry in electrical charge, distribution of electronic charge around an atom changes with time and at any instant the charge distribution is not perfectly symmetric: there are regions of partial positive charge and partial negative charge. Resulting attraction between two atoms through electrostatic interactions.

Dipole-dipole- polarity, regions of the molecule with partial charges/dipoles, favorably interact with ions.

• H-bonds are the strongest

• Must be able to draw H bonds between molecules such as water and amino acids

What is the primary reason why nonpolar molecules cluster together in water?

Hydrophobic effect- when a nonpolar molecules is in water, this disrupts some hydrogen bonds between water molecules. The water molecules reorient themselves to form the maximum amount of H bonds, but the water molecules around the nonpolar molecule are more ordered then elsewhere in the solution. Nonpolar solute molecules are driven together in water not primarily because they have a high affinity for each other but because when they do associate, they disorder water molecules.

Hydrophobic interactions form spontaneously and increase the entropy of water

Example- phospholipid bilayer

What does it mean for a molecule to be amphipathic?

It has both hydrophobic and hydrophilic parts

Explain how proteins can spontaneously fold to form structures that are more ordered

Hydrophobic effect- nonpolar amino acids associate together in the interior of the folded protein, creates an increased entropy in water to compensate for entropy losses in the folding process

Chemical equation for the autoionization of water

H2O —> H+ + OH-

Define Ka. What is the difference between a compound with a large Ka versus one with a small Ka

Ka- the acidity constant, a measure of the strength of an acid in a solution, measures the extent to which an acid breaks apart into its component ions when dissolved in water

High Ka= strong acid, low Ka=weak acid

henderson-Hasselbalch equation

PH= pka + log ([A-]/[HA])

When PH equals pKa, the concentration of the acid and its conjugate base are equal, and the acid is half protonated and half deprotanated

must be able to draw a titration curve for a given acid

When pH<PKa more [HA], more acidic, equilibrium to the right leads to increase in H+

When pH>Pka more [A-'], more basic, equilibrium to the left leads to less H+

What conjugate acid/base pair acts as a major buffer in blood?

Buffers- resist changes in pH, have an inflection point in a titration curve, weak acids are most effective in buffering

CO2 + H2O —> H2CO3 —> H+ + HCO3-

Why are transient interactions important for life?

Transient interactions- temporary reversible associations between molecules, most notably proteins that easily form and break apart within cells.

Important for function, communication, and response to changes in the environment

Ionic interactions

electrostatic interactions between permanently charged species/colombic interactions

electrostatic interactions between an ion and a permanent of induced charge

Can contribute 12-20 kJ/mol of stability to a folded protein or to a ligand-receptor interaction

• dielectric constant- reflects the ability of the solvent to keep opposite charges apart

• dielectric constant for water is high because it has strong ion dipole interactions that keep molecules apart, can form a hydration shell around ions

What drives the formation of the double helix?

• Ionic interactions between phosphate groups on DNA- repulsive, destabilize and oppose the formation of the double helix

• Hydrogen bonds form between base pairs and between nitrogenous bases and H2O- favors single stranded DNA and double stranded DNA

• Van der waals- between base pairs stabilize the double helical structure through pi stacking, minerly contribute to ssDNA

• Hydrophobic effect- double stranded

Overall- ionic interactions, hydrogen bonds, and van der waals interactions contribute to delta H, and hydrophobic effect contributes to delta S (entropy of DNA)

Overall entropy of DNA favors single stranded

note- forming interactions involve negative enthalpy

Hydrogen bonds

partially covalent interaction between a hydrogen bond donor and a hydrogen bond acceptor- typically O, N

4-20 kJ/mol

Van der waals interactions

weak interactions between all atoms due to the fact that distribution of electronic charge around an atom changes with time

attractive (london dispersion) and repulsive (steric) components

2-4 kJ/mol atom pair- individually weak but additive

Van der wals contact distance- optimal separation between 2 molecules where attractive forces are maximized, and repulsive forces begin to dominate

Hydrophobic effect

refers to the association of nonpolar molecules in aqueous solution

NOT due to any intrinsic interaction between nonpolar moieties

plays a significant role in

• protein folding

• formation of lipid bilayers

• ligand binding

release of ordered water molecules drives formation of an enzyme-substrate complex

nonpolar molecules aggregate to maximize surface area exposed to water, overall reduces the hydrophobic surface area and the number of water molecules that are ordered and form the cage around them, entropy increased

Solvation of a crystalline salt

Ion-dipole interactions maximize the ion dipole interactions between ions and water- water orientation is non random around charge= loss in entropy

Weak forces stabilize the double helix

Cooperativity- a phenomenon that occurs when multiple parts of a system act together even though they appear to be independent, through communication and physical contact

DNA denaturation- monitor how easily DNA unwinds, base pairs talk to each other and coordinate to make unwinding more easy

• melting curve- S-shaped curve shows cooperativity, Base pairs at ends exposed, H bond donors/acceptors exposed and can bind with H2o facilitates unwinding

• Tm- melting temperature of DNA the point where 50% is in dsDNA form

• must be able to draw thermal denaturation melting curve

What does p mean

-log

one pH unit equals a factor of 10 in H+- logarithmic scale

acidic solutions have a high H+ concentration and low pH values

Weak acids

primarily in biological systems, incomplete dissociation in aqueous solutions

Ka

Ka= [H+][A-]/[HA]

Low Ka means high reactants, the higher the Ka the weaker the acid

Buffer

An aqueous solution of a weak acid/conjugate base pair that resists a change in pH when additional acid or base is added.

When more acid is added H+ reacts with base to form more weak acid

changes ratio of A- to HA without significantly impacting pH

Must have high concentrations of both HA and A-, buffering range ± 1 pH unit around the pka