Biochemistry midterm

A polar molecule is one in which one end is partially positive and the other partially negative.

• Ionic interactions
• hydrogen bonding
• Van der Waals

• dipole-dipole
• dipole-induced dipole
• induced dipole-induced dipole

Ionic interactions occur between charged atoms or groups.

Water molecules hydrogen bond with each other. Four bonding attractions occur.

Energy to vaporize 1 mole of water at 1 atm

Energy to change temperature by 1 degree C

Nonpolar molecules have no polar bonds or the bond dipoles cancel due to molecular geometry. These molecules do not form good attractions with the water molecule. They are insoluble and are said to be hydrophobic (water hating).

When there is too much salt on the outside of the cell, so the cell losses water and shrinks.

The proton donor

The proton acceptor

The equilibrium expression for a weak acid.

A solution that resists change when a small amount of strong acid or strong base is added.

phosphate buffer

A compound with both positive and negative charges.

Equal moles of acid are equal to moles of salt

Equal amounts of acid and base are in a solution

The heat and energy transformations studied by thermodynamics take place in a system (defined by investigator) connected to the surroundings (the rest of the universe)

Energy exchanges between system and surroundings

Matter and energy exchanged between system and surroundings

• Energy is neither created nor destroyed
• deltaE = q+w
• deltaE is the change in the internal energy and is a state function
• q is heat
• w is work

Biochemical systems

deltaH reactants = deltaH products - deltaH reactants

• -deltaH is exothermic
• +deltaH is endothermic

• With a spontaneous reaction, the entropy of the universe increases.
• deltaS univ = deltaS system + delta s surroundings

Gibbs free energy change (deltaG)

• Free energy decreases
• deltaG is negative energy released by the reaction
• said to be exergonic

• Free energy increases
• deltaG is positive energy absorbed by the reaction
• said to be endergonic

• Two reactions run as a pair.
• One is endergonic and the other is exergonic.
• Overall it is exergonic and the pair is spontaneous

Hydrolysis of ATP

• A carboxylic acid with an amino group on the carbon alpha to the carboxylic acid
• The alpha carbon also has an R group side chain. (except glycine which has two H's)

Enantiomeric

a peptide bond

• nonpolar
• polar
• acidic
• basic

• negatively
• positively

How the amine and carboxyl groups react with the hydrogen ion

protonated

When there is no net charge