L2 - thermodynamics

• Living creatures are merely chemical systems.
• Organic compounds are the basis for life as they bring order to chemical reactions in cells.
• Cell components include proteins, nucleic acids, lipids, and carbohydrates.
• Cell chemistry is complex as there are many interlink networks of chemical reactions.
• 99% of the total number of atoms in cells are made from C, H, N, O.
• 90 % of the total number of atoms in cells are made from P, Cl, S, Na, Mg, K, Ca.
• Chemical groups include methyl (-CH3), hydroxyl (-OH), carboxyl (-COOH), carbonyl (-C=O), phosphate (-), sulfhydryl (-SH), amino (-NH2).
• Carbon is important because it has many states, meaning it can lead to many different functions.
• Carbon can form four covalent bonds with other atoms, allowing it to form large and complex molecules.
• Organic compounds are those with carbon.
• Bond strength is related to the amount of energy needed to break it.
• Covalent bonds are formed between the monomers to form polymers, are 100 times stronger than non-covalent bonds, resist being pulled apart by thermal motions, and can only be broken by biologically catalyzed chemical reactions.
• Non-covalent bonds are formed between different polymers to form macromolecular assemblies, are transient, and provide flexibility to regulate biochemical processes.
• Hydrogen bonds are any bond formed with hydrogen, can be H-O, H-N.
• Organic compounds, also known as molecules and macromolecules, are carbon based and found in free solution.
• ATP is released through ATP hydrolysis.
• Oxidation and reduction require electron transfer.
• ATP is the most used activated carrier, and synthesis of biological polymers uses the energy in chemical bonds.
• Acetyl coA is also an electron carrier, and it has a thioester bond that works like the phosphates of ATP, giving acetyl group instead of phosphate.
• Reactions in cells are coupled to ensure that the change in free energy of the coupled reactions is less than 0.
• If our body does not have enzymes, the chemical reactions needed for the cell to survive would not be fast enough to keep our cells alive.
• Equilibrium is reached when the number of Y (reactants) is equal to the number of X (products).
• Oxidation is the removal of electrons from an atom (partially + charge).
• Reduction is the addition of electrons from an atom (partially - charge).
• Reduction occurs when the number of C-H bonds increases than the molecule is reduced.
• Enzymes cannot force energetically unfavorable reactions to occur.
• Hydrogenation is when a molecule picks up an electron and a hydrogen.
• NADH and NADPH are also electron carriers.
• Enzymes catalyze an already favorable reaction by lowering activation energy to make the reaction to occur, speeding up the reaction.
• NADP is a carrier.
• Energy of sunlight is converted into useful bond energy.
• There are four major families of organic compounds in the cell: fatty acids, sugar, amino acid, and nucleotide.
• All molecules have an additional function which is that they store energy of the cell and this energy can be used for other pathways in the cell.
• Ethalpy is the energy that can be released from chemical bonds.
• Living cells create and maintain order, performing never ending streams of chemical reactions.
• Amino acids are found in proteins, which are versatile and can act as enzymes that catalyze the formation and breaking of covalent bonds.
• Gibbs free energy: < 0 is energetically favorable, can occur spontaneously, loss of free energy, reduction of order (increase in S) > 0 is energetically unfavorable, can only occur if coupled with a second energetically favorable reaction.
• Cell heat comes from food we ingest, which is stored in the chemical bonds of organic molecules.
• The assembly of macromolecules is done through a sequence, with subunits added in a precise order.
• Metabolic cellular processes can be either anabolic, which is energetically unfavorable and results in condensation, or catabolic, which is energetically favorable and results in hydrolysis.