Chapter 2: Physical Biochemistry

Question 1

Thermonuclear fusion

Answer 1

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

Question 2

Covalent bond formation

Answer 2

When two molecules have a large enough difference in electronegativity to bond to each other.

Ex. H2O CO2

Question 3

Photosynthesis

Answer 3

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

Question 4

What are Coupled Oxidation Reduction Reactions?

Answer 4

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

Question 5

Reduction vs Oxidation

Answer 5

Reduction is the gain of electrons
Oxidation is loss of electrons

Question 6

Oxidation Reduction Reaction Examples:

Answer 6

Light is used for ATP and NADPH synthesis

Question 7

ATP

Answer 7

Adenine tri-phosphate is an energy source that is used for metabolic processes and can converted to ADP and back to ATP

Question 8

1st Law of Thermodynamics

Answer 8

Energy in the universe remains the same:
ΔE = E(final)-E(initial)= q(heat) + w(work)

Question 9

Enthlapy

Answer 9

ΔH = ΔE +ΔPV
(Pressure and volume are negligible in Biochem)

Question 10

Calorimeter

Answer 10

Measures the ΔH or change in heat. Units are Joule or calorie
1 calorie = 4.184 J

Question 11

2nd Law of Thermodynamics

Answer 11

All spontaneous reactions tend toward dispersal of energy which increases Entropy
Ex:oxidation of glucose into 6h2o and 6co2 increases entropy

Question 12

Gibb’s Free Energy

Answer 12

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

Question 13

Endergonic vs Exergonic

Answer 13

Endergonic: Intakes energy (cold)
ΔG>0, Unfavorable reaction
Exergonic: release energy (hot)
ΔG<0, favorable reaction

Question 14

Spontaneity of a Reaction

Answer 14

Question 15

Relation Between Gibb’s and Keq

Answer 15

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

Question 16

(Cellular) Gibb’s Equation

Answer 16

Because concentrations are typically in mm(10^-3) or um (10-6)
ΔG = ΔG’ + RT(lnQ)
if Rxn is at equilibrium:
ΔG’ = RT(lnQ)

Question 17

What are three types of Weak non-covalent bonding

Answer 17

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

Question 18

What role does Polarity play in water

Answer 18

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

Question 19

What are antifreeze proteins

Answer 19

They are small proteins that interact with small ice crystals to prevent further crystallization. This is useful for organisms that live in cold environments

Question 20

What are salt bridges

Answer 20

Ionic Bond

Question 21

Describe Hydrophilic and hydrophobic effects

Answer 21

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

Question 22

What causes hydrophilic or hydrophobic effects?

Answer 22

Hydrophobic caused by a decrease in Entropy (ΔS)
Hydrophilic does not decrease Entropy

Question 23

How do hydrophobic and hydrophilic effects influence ΔG

Answer 23

Hydrophobic lowers ΔG
Hydrophobic bodies joining increases entropy
ΔG = ΔH - TΔS

Question 24

What is a coupled reaction? What is an Example?

Answer 24

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

Question 25

What relationship is observed in a buffer system regarding the abundance of an acid? (Buffer graph)

Answer 25

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