Thermodynamics and Equilibrium (L1)

Question 2

What are the 3 main factors that dictate cell chemistry?

Answer 2

1. Life depends on chemical reactions
2. Most of the carbon present are incorporated into macromolecules (allow cells to grow and function)
3. Cell chemitry is VERY complex

Question 3

What are the 2 main types of chemical interactions?
Give properties of both

Answer 3

Covalent and non-covalent

• Covalent = 100x Stronger than non-covalent
• Covalent bonds form macromolecules
• Covalent bonds NOT broken by thermal motion, only broken by biologically CATALYSED chemical reactions
• Non-covalent bonds allow molecules to recognize each others and reversibly associate

Question 4

What are atoms proportions in the cell?

Answer 4

99% = C, H, N, O
0.9% = P, S, Cl, Na, Mg, K, Ca

Question 5

Name the abundant chemical groups present in cells. (7)

Answer 5

• Methyl (-CH3)
• Hydroxyl (-OH)
• Carboxyl (-COOH)
• Carbonyl (-C=O)
• Phosphate (-PO3 -2)
• Sulfhydryl (-SH)
• Amino (NH2)

Question 6

How are carbon compounds made by cells called?

Answer 6

Organic molecules
Important for the richness of forms and functions of the molecules bc C-C is a stable bond capable of forming large complex molecules (chains or rings)

Question 7

What is an organic compound?
What are the 4 major families of compounds and their characteristics?

Answer 7

• Carbon based (30 carbons)
• Found in free solution (aqueous?)
• Organic compounds assemble to form macromolecules

4 major families:
- Sugar (-OH)
- Amino Acids (-CH3)
- Fatty Acids (-COO-)
- Nucleotides (-NH2 amino and PO4 -2 phosphate)

Question 8

What is the main use of organics compounds in life?

Answer 8

1. They are the monomer subunit for Polymeric Macromolecules
2. Energy sources when covalently bonded to each other forming macromolecules

Question 9

What different macromolecules are formed from assembly of organic compounds?

Answer 9

Sugars → polysaccharides, glycogen, starch (in plants)
Fatty acids → fats and membrane lipids
Amino Acids → Proteins
Nucleotides → Nucleic Acids

*Covalently linked organic molecules, breaking these bonds releases energy

Question 10

What are the roles of covalent and non-covalent bonds in assembly of macromolecules?

Answer 10

Covalent bonds → allows rotation → flexibility → several conformations

Non-covalent bonds → allow assembly of macromoluecule and constrain shape to one conformation

Organic compound subunits → macromolecules (obtained by covalent bonds)→ macromolecular assembly (obtained by non-covalent bonds)

Question 11

What are the 2 major types of reactions responsible for the cell metabolism?

Answer 11

1. Anabolic pathway
   A-H + HO-B → A-B
   CONDENSATION (H2O leaves), energetically unfavourable
2. Catabolic pathway
   A-B → A-H + HO-B
   HYDROLYSIS (energetically favourable, energy from A-B bond is released)

Question 12

What is the difference in the tendencies of the reactions in living cells vs nonliving matter?

Answer 12

Living cells → Create and Maintain Order → Perform never ending stream of chemical reactions (all catalysed)

Nonliving matter → Universe tends to greater disorder

Question 13

What does the 2nd law of thermodynamics state?

Answer 13

For any ISOLATED system, the degree of disorder always increases
(Ever increasing entropy)

The most probable arrangement is the most disorder (less energy needed juts like clean vs dirty room)

Question 14

What is entropy (S) defined as?

Answer 14

It is a measure of the amount of disorder in a system
The greater the disorder, the greater the entropy
System will spontaneously change towards an arrangement with greater S

Question 15

How is it possible that cells generate order to function based on 2nd law of thermodynamics?

Answer 15

Cell must not be an isolated system as they decrease entropy by generating order and in an isolated system, entropy is ever increasing
Another sub-system in the same isolated system as the cell must release energy for the cell to use and for total S to increase

Question 16

Where does the cell heat come from? (The heat is uses to generate order)

Answer 16

From food molecules —> Catabolic Pathway (heat is released unless used to creare more order in the cell) —> building blocks for biosynthesis (organic compounds) —> Anabolic Pathways (with energy from catabolic) —> molecules that form the cell

Question 17

What are the 3 main uses for organisms, of the energy the organisms extract by breaking chemical bonds?

Answer 17

• Live
• Grow
• Reproduce

Question 18

What does the first law of thermodynamics state? Explain how it applies to plants.

Answer 18

The energy cans be converted from on form to another but cannot be created of destroyed
ex with plants:
Energy of sunlight —> photosynthesis —> sugars —> chemical bond energy —> cellular respiration
*Energy is stored and maintained in chemical bonds

Question 19

What is enthalpy?

Answer 19

Enthalpy is the energy than can be released from chemical bonds
- Negative enthalpy change (Hf - Hi) is spontaneously favourable

Question 20

What is Gibbs free energy equation?

Answer 20

∆G = ∆H - T∆S
Energically favourable when ∆G < 0 —> ∆H < T∆S
*When S increases (more entropy) and H decreases (les energy in final bonds)

Question 21

How can energetically unfavourable reaction occur?

Answer 21

When they are coupled to energitically favoured reaction that can provide them energy

Question 22

What is the importance of enzymes in chemical reactions?

Answer 22

They catalyse the reactions by lowering the activation energy required for the reaction to take place
I takes less time for the reactants to reach the required activation energy —> speeds up the reaction
*Even energetically favourable reaction need a push to surpass energy of activation

Question 23

What is the most used activated carrier?

Answer 23

ATP
Brings energy from catabolic (favourable) to anabolic (unfavourable) pathway

Question 24

What is the standard free energy formula?

Answer 24

∆G˚ = ∆G + TRln([X]/[Y])
*[X]/[Y] —> equilibrium cste

Question 25

Give an example of a reaction driven by ATP hydrolysis.

Answer 25

Step 1:
A-OH + ATP → A-O-P + ADP

Step 2: (condensation)
A-O-P + B-H → A-B + inorganic P

ex: Glutamic acid (A-OH) → glutamine (A-NH2), where B-H is ammonia NH3

Question 26

What is Acetyl CoA?

Answer 26

Acetyl group (H3C-C=O) –high-energy bond– coenzyme A (CoA) / Handle

high-energy bond = Thioester bond

*releases energy and acetyl group by breaking the bond

Question 27

What is an oxidation reaction?

Answer 27

Removal of electrons from an atom (partial +ive charge)
- Catalysed reaction
- Addition of more Oxygen in the molecule (rarely happens)

Question 28

What is a reduction reaction?

Answer 28

Addition of electrons to an atom (partial (-)ive charge)

Hydrogenation = Reduciton
If # C-H bonds increases, molecule is reduced

Question 29

What are the most important electron carriers?

Answer 29

NADH and NADPH
*Carries electrons between coupled oxidation and reduction reactions

NAD+ = Nicotinamide adenine dinucleotide
NADP+ = Nicotinamide adenine dinucleotide phosphate

Question 30

What is the Structure of NADP+?
What is the difference between NAD+ and NADP+?

Answer 30

• 2 nucleotides linked by diphosphore bond between two 5’ phosphates
• Bottom one has 2’ phosphate + 1’ Adenine
• Top one has nicotinamide ring that can take and H

The 2’ phosphate linked to the Ribose is not there in NAD

Question 31

Name the group carried in high-energy linkage for in ATP, NADH, NADPH, FADH2, Acetyl CoA, Carboxyl biotin, S-adenosylmethionine, Uridine diphosphate glucose?

Answer 31

ATP = Phosphate
NADH, NADPH, FADH2 = electrons and hydrogens
Acetyl CoA = Acetyl group
Carboxyl biotin = Carboxyl group
S-adenosylmethionine = Methyl group
Uridine diphosphate glucose = glucose