Thermodynamics and Equilibrium (L1) Flashcards
What are the 3 main factors that dictate cell chemistry?
- Life depends on chemical reactions
- Most of the carbon present are incorporated into macromolecules (allow cells to grow and function)
- Cell chemitry is VERY complex
What are the 2 main types of chemical interactions?
Give properties of both
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
What are atoms proportions in the cell?
99% = C, H, N, O
0.9% = P, S, Cl, Na, Mg, K, Ca
Name the abundant chemical groups present in cells. (7)
- Methyl (-CH3)
- Hydroxyl (-OH)
- Carboxyl (-COOH)
- Carbonyl (-C=O)
- Phosphate (-PO3 -2)
- Sulfhydryl (-SH)
- Amino (NH2)
How are carbon compounds made by cells called?
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)
What is an organic compound?
What are the 4 major families of compounds and their characteristics?
- 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)
What is the main use of organics compounds in life?
- They are the monomer subunit for Polymeric Macromolecules
- Energy sources when covalently bonded to each other forming macromolecules
What different macromolecules are formed from assembly of organic compounds?
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
What are the roles of covalent and non-covalent bonds in assembly of macromolecules?
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)
What are the 2 major types of reactions responsible for the cell metabolism?
- Anabolic pathway
A-H + HO-B → A-B
CONDENSATION (H2O leaves), energetically unfavourable - Catabolic pathway
A-B → A-H + HO-B
HYDROLYSIS (energetically favourable, energy from A-B bond is released)
What is the difference in the tendencies of the reactions in living cells vs nonliving matter?
Living cells → Create and Maintain Order → Perform never ending stream of chemical reactions (all catalysed)
Nonliving matter → Universe tends to greater disorder
What does the 2nd law of thermodynamics state?
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)
What is entropy (S) defined as?
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
How is it possible that cells generate order to function based on 2nd law of thermodynamics?
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
Where does the cell heat come from? (The heat is uses to generate order)
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
What are the 3 main uses for organisms, of the energy the organisms extract by breaking chemical bonds?
- Live
- Grow
- Reproduce
What does the first law of thermodynamics state? Explain how it applies to plants.
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
What is enthalpy?
Enthalpy is the energy than can be released from chemical bonds
- Negative enthalpy change (Hf - Hi) is spontaneously favourable
What is Gibbs free energy equation?
∆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)
How can energetically unfavourable reaction occur?
When they are coupled to energitically favoured reaction that can provide them energy
What is the importance of enzymes in chemical reactions?
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
What is the most used activated carrier?
ATP
Brings energy from catabolic (favourable) to anabolic (unfavourable) pathway
What is the standard free energy formula?
∆G˚ = ∆G + TRln([X]/[Y])
*[X]/[Y] —> equilibrium cste
Give an example of a reaction driven by ATP hydrolysis.
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
What is Acetyl CoA?
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
What is an oxidation reaction?
Removal of electrons from an atom (partial +ive charge)
- Catalysed reaction
- Addition of more Oxygen in the molecule (rarely happens)
What is a reduction reaction?
Addition of electrons to an atom (partial (-)ive charge)
Hydrogenation = Reduciton
If # C-H bonds increases, molecule is reduced
What are the most important electron carriers?
NADH and NADPH
*Carries electrons between coupled oxidation and reduction reactions
NAD+ = Nicotinamide adenine dinucleotide
NADP+ = Nicotinamide adenine dinucleotide phosphate
What is the Structure of NADP+?
What is the difference between NAD+ and NADP+?
- 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
Name the group carried in high-energy linkage for in ATP, NADH, NADPH, FADH2, Acetyl CoA, Carboxyl biotin, S-adenosylmethionine, Uridine diphosphate glucose?
ATP = Phosphate
NADH, NADPH, FADH2 = electrons and hydrogens
Acetyl CoA = Acetyl group
Carboxyl biotin = Carboxyl group
S-adenosylmethionine = Methyl group
Uridine diphosphate glucose = glucose
