Unit 1 - Chemical Foundations of Biochemistry

Biochemistry

Study of chemical processes and transformation of living organisms

Living Systems

Maintains organized states that goes against EQ, using constant exchange of matter and nrg, and after death, system moves to environment’s EQ

Origin of Life determined with

1. Direct observations of reactions, chemistry

2. Experimental tests

3. Historical reconstruction

Correct Data doesn’t guarantee a

Correct Interpretation (antifreeze proteins)

First Law of Thermodynamics

Energy (U) is conserved

Enthalpy Formula

U + PV = q

Second Law of Thermodyanmics

Entropy (S) tends to increase

Entropy Formula

k_blnW

If G > 0

Energonic and non spontaneous

Reduction

Gaining electron, adding H₂ or removing O₂

Oxidation

Adding O₂, removing H₂

How much are humands made out of water?

60%

Water can hydrogen bond upto

Four times

How long do hydrogen bonds last?

10^-12 seconds

Dipole Dipole Interactions

Interaction btwn polar (not charged) groups

Dipole Induced Dipole

Interaction between a polar and nonpopular molecule

How long are covalent bonds?

1A

How long are hydrogen bonds?

1.8A

How long are van der waals bonds?

2.7A

Dielectric Constant

Solvents ability to diminish the electrostatic attractions btwn dissolved ions

Why is the hydrophobic effect spontaneous?

Clumping of hydrophobic molecules decreases SA of H₂O molecules in contact, allowing more fluidity of surrounding H₂O molecules (-S) and hydrophobic things break hydrogen bonding (+H)

Proton Jumping

H⁺ moves through a network of H-bonding molecules by shifting covalent bonds than diffusing as a whole ion

pH of human blood

7.4

pH of pancreatic juice

7.8 - 8

pH of blood

7.0

pH of saliva

6.4 - 7

pH of urine

5.0 - 8.0

pH of gastric juice

1.5 - 3.0

In a low pKa

Most molecules are unprotonated (no H)

In a high pKa

Most molecules are protonated (H)

H₃PO₄ pKa

2.15

H₂PO₄^- pKa

6.82

HPO₄^2- pKa

12.38

In a pH below 2.15, what is the dominate form of phosphoric acid?

H₃PO₄

In a pH between 2.15 - 6.82, what is the dominate form of phosphoric acid?

H₂PO₄^-

In a pH between 6.82 - 12.38, what is the dominate form of phosphoric acid?

HPO₄^2-

In a pH above 12.38 what is the dominate form of phosphoric acid?

PO₄^3-

Bicarbonate Buffer

H₂O + CO₂ = H₂ CO₃ = H⁺ + HCO₃

What happens if blood is too acidic?

Exhale CO₂

What happens if blood is too basic?

Increase CO₂

Bicarbonate Reabsorption

H⁺ leaves kidney in exchange for Na⁺, and combines with HCO₃to make CO₂

Bicarbonate Production

Carbonic acid derived from H⁺ is pumped out of the kidney and leftover HCO₃ is exchanged for Cl^-