water and buffers

Electronegativity of water

Partial negative charge on oxygen and partial positive charge of hydrogen making it polar

Hydrogen bond

A non covalent interaction

A Hydrogen bond is how long?

3 A

A hydrogen bond is strongest at what angle?

180

Hydrogen bonds form when

Hydrogen is covalently bound to a electronegative atom (O,N)

Water disrupts hydrogen bonds between

Biological molecules

Why are weak non covalent interactions important for structure and function of bio molecules?

Weak interactions can form and dissociate allowing for processes like DNA replication and transcription

Van der waals

A weak non covalent interaction where electronic charge distribution around atom is not symmetrical

Van der waals and distance

At far distance, there is little energy between them. As they get closer, they reach the contact distance and both atoms have asymmetric charges that form interaction. If forced closer together then they will be repulsed

Van der waal interactions in geckos

Hairs extend off their foot into spatulae. Due to the sheer number of VDW it can hold the weight of the gecko and can break and reform

Ionic bonds

A weak non covalent interaction between distinct electrical charges

Electrostatic energy formula

E = kq1q2/Dr

Dielectric constant and energy

Higher the dielectric constant, the less energy (water has high D constant so it has less energy bc it’s polar and can surround molecules to prevent interactions)

Hydrophobic effect

Spontaneously the Non polar molecules come together and water forms a cage around it

Second law of thermodynamics

The entropy of the universe is always increasing (always going toward a system where molecules are disrupted)

What happens to entropy after the hydrophobic effect takes place?

Increases

Amphipathic lipids

Some parts are polar and some non polar

What drives the formation of phospholipid bilayers?

Hydrophobic effect

Covalent bonds

Stable and harder to break

Non covalent bonds

Weaker and allow formation and breakage and are additive

pH formula

pH = -log[H+]

pH + pOH = ?

14

Kw = [H+][OH-]

(10^-7) (10^-7) = 1.0 × 10^-14

Henderson hasselbalch equation

pH + pka + log ([A-]/[HA])

When conjugate base equals conjugate acid then pH

Is equal to the pka

When pH is below the pka

Conjugate acid predominates

When pH is above the pka

Conjugate base predominates

Buffers

An acid base pair that can resist changes in pH

Pka formula

Pka = - log(Ka)

Protic acids can have multiple

Ka values

Why are biological systems generally buffered?

A sudden shift in pH would change protein quality.

Why should you select a buffer with a pka value close to the desired pH of the system?

Equal amount of conjugate acid and base maintains the buffer then pH=pka

Ka formula

10^-pka = ka