Chapter 2: Physical Biochemistry Flashcards
Thermonuclear fusion
A process in which autotrophs use solar energy from the sun to carry out reactions such as carbon fixation and anerobic respiration necessary for metabolism
Covalent bond formation
When two molecules have a large enough difference in electronegativity to bond to each other.
Ex. H2O CO2
Photosynthesis
The process by which plants are able to use Solar energy as a way to generate carbohydrates that work as energy to carry out metabolism
What are Coupled Oxidation Reduction Reactions?
A series of linked Oxidation-Reduction reactions which transfer electrons from one compound to another.
Chemical work is performed resulting in the generation of energy
Reduction vs Oxidation
Reduction is the gain of electrons
Oxidation is loss of electrons
Oxidation Reduction Reaction Examples:
Light is used for ATP and NADPH synthesis
ATP
Adenine tri-phosphate is an energy source that is used for metabolic processes and can converted to ADP and back to ATP
1st Law of Thermodynamics
Energy in the universe remains the same:
ΔE = E(final)-E(initial)= q(heat) + w(work)
Enthlapy
ΔH = ΔE +ΔPV
(Pressure and volume are negligible in Biochem)
Calorimeter
Measures the ΔH or change in heat. Units are Joule or calorie
1 calorie = 4.184 J
2nd Law of Thermodynamics
All spontaneous reactions tend toward dispersal of energy which increases Entropy
Ex:oxidation of glucose into 6h2o and 6co2 increases entropy
Gibb’s Free Energy
The difference between enthlapy (H) and the entropy (S) at a given temp
ΔG = ΔH - TΔS
standard conditions are 298K and 1atm
For Biochem: (pH = 7, h2o constant [55M])
ΔG’ = ΔH - TΔS
Endergonic vs Exergonic
Endergonic: Intakes energy (cold)
ΔG>0, Unfavorable reaction
Exergonic: release energy (hot)
ΔG<0, favorable reaction
Spontaneity of a Reaction
Relation Between Gibb’s and Keq
ΔG = RT(lnKeq)
R is gas constant 8.314 kJ/mol
T is absolute temp in Kelvin
If Keq is less than one, reactants are favored
(Cellular) Gibb’s Equation
Because concentrations are typically in mm(10^-3) or um (10-6)
ΔG = ΔG’ + RT(lnQ)
if Rxn is at equilibrium:
ΔG’ = RT(lnQ)
What are three types of Weak non-covalent bonding
Van Der Waal Forces:
- Bond energy 1-10 kJ/mol
- Force generated by unequal electron sharing
- Bond strength dependent on distance of one molecule to the other, not too close or too far
Hydrogen Bonding:
-Occur between H atoms on an electronegative donor and another electronegative acceptor
- Bond energy 10-30 kJ/mol
-strength varries by bond angle
Ionic Bonding: (Salt Bridges)
- Interactions between oppositely charged molecules
- Affected by distance but not angle
- 20-80 kJ/mol
What role does Polarity play in water
Water is polar and can form 4 hydrogen bonds with other water molecules leading to many of water’s properties
Water has lower density as solid (.92 vs 1.0)
Water has high heat capacity
Water is bonded to on average 3.4 molecules of water
What are antifreeze proteins
They are small proteins that interact with small ice crystals to prevent further crystallization. This is useful for organisms that live in cold environments
What are salt bridges
Ionic Bond
Describe Hydrophilic and hydrophobic effects
Hydrophobic:
- Fats or CH chains that are not water soluble
- Result in cage formations
- Do not form H bonds with water (decreases entropy)
- Play important role in protein folding
- Will attempt to join with other hydrophobic masses to increase entropy
- Ex. Limonene
Hydrophilic:
- Will form H bonds with water
- Allow for water to bond at many points which does not decrease entropy
- Can fold in proteins leading to coverage of hydrophobic parts
- Ex. Glucose
What causes hydrophilic or hydrophobic effects?
Hydrophobic caused by a decrease in Entropy (ΔS)
Hydrophilic does not decrease Entropy
How do hydrophobic and hydrophilic effects influence ΔG
Hydrophobic lowers ΔG
Hydrophobic bodies joining increases entropy
ΔG = ΔH - TΔS
What is a coupled reaction? What is an Example?
If a reaction is endergonic and unfavorable it can be exergonic and coupled to make it more favorable
An example is ATP hydrolysis(exergonic) has a ΔG’ = -30.5 kJ/mol which can then be used to generate Glutamate and NH4 creating Glutamine
What relationship is observed in a buffer system regarding the abundance of an acid? (Buffer graph)
On the bottom left, the most hydrogenated molecules are abundant
In the middle there is a balance of charges
On the top right, the most negatively charged molecules are abundant
