Cell chemistry and Bioenergetics Lectures Flashcards
What are the properties of chemical bonds?
- Bond strength -> amount of energy needed to break it
- Covalent bonds are 100x stronger than non-covalent bonds
- Covalent bonds form macromolecules
- Covalent bonds resist being pulled apart by thermal motions
- Covalent bonds only broken by biologically catalyzed chemical reactions
- Non-covalent bonds allow molecules to recognize each others and reversible associate
Describe the chemical components of the cell?
- 99% total number of atoms in the cell: C, H, N, O’
- 0.9% total number of atoms in the cell: P, S, Cl, Na, Mg, K, Ca
Popular Combinations:
- Methyl (CH3)
- Hydroxyl (-OH)
- Carboxyl (-COOH)
- Carbonyl (C=O)
-Phosphate (-PO3^-2)
- Suflhydryl (-SH)
- Amino (-NH2)
How are cell compounds formed?
- Carbon atoms can form four covalent bounds with other atoms -> high ability to form macromolecules
- C-C stable bonds form chains and rings -> generate large and complex molecules
- Carbon compounds made by cells -> organic compounds
- A few categories of molecules give rise to all extra extraordinary richness of form and function
Where are organic compounds found? What are they based with?
- They are carbon based (around 30 carbons)
- They are found in free solution
- Compounds in the cell are chemically related and classified in 4 major families of compounds
What are the uses of organic compounds?
1) Monomer subunits to construct Polymeric Macromolecules
2) Energy sources -> broken down and transformed into other small molecules (used in metabolic pathways)
3) Many have both functions (subunits and energy sources)
4) Organic molecules are synthesized or broke down into the same set of simple compounds
What macromolecules do the following organic compounds form:
1) Sugars
2) Fatty Acids
3) Amino Acids
4) Nucleotides
1) Polysaccharides, glycogen and starch (in plants)
2) Fats and membrane lipids
3) Proteins
4) Nucleic Acids
What is a macromolecule?
- Most abundant carbon containing molecules
- Principle building and functional blocks of cells
- Made by covalently linked organic molecules (monomers) into chains
- Sugar/amino acid: versatile and perform thousands of functions, Enzymes catalyze formation and breaking of covalent bonds
- Nucleic acid -> DNA and RNA
How do macromolecules assemble?
The subunits are added in a precise order and they are very organized to account for specific conformation anf function.
The covalent bonds are flexible and rotate - there are several different conformations.
There are not several different conformations for non-covalent bonds.
Non-covalent bonds allow macromolecules to interact with each other - they constrain shape to one conformation.
What are the two types of reactions for cell metabolism?
1) Anabolic Pathway: two monomers put together through covalent bonding - need to provide energy to make bonds.
Energetically unfavourable.
2) Catabolic Pathway: break bonds and make monomers - release energy when bonds are broken.
Energetically favourable.
What is the second law of thermodynamics?
- In any isolated system the degree of disorder always increases. The mot probably arrangement is the most disorder (if there is no energy in the system)
- Amount of disorder in any system is quantified and express as the ENTROPY (S) –> The greater the disorder the greater the entropy –> Systems will change spontaneously towards arrangements with Higher S.
How is it possible that the release of heat energy enables cell order?
You need to consider a cell a non-isolated system. It has an environment. Interactions inside the cell have order and also release heat to its environment. It warms up the environment. And when the liquid has heat, the molecules move faster and it creates disorder.
Where does the cell heat come from?
It comes from food.
What is the first law of thermodynamics?
The energy can be converted from one form to another but cannot be created or destroyed. In biological systems, energy is stores and managed with chemical bonds. A negative enthalpy change (Hf-Hi) spontaneously favorable reaction.
What is Gibbs free energy?
G = H-TS
- Gibbs free energy, denoted G, combines enthalpy and entropy into a single value. The change in free energy, ΔG, is equal to the sum of the enthalpy plus the product of the temperature and entropy of the system.
PUTTING it all together!
What is the effect of enzymes in a reaction?
Enzymes catalyze the reaction by lowering the activation energy required for a reaction to take place. It then takes less time for the reactants to reach the required activation energy, therefore speeding up the reaction.
Enzymes speed up reactions but cannot force energetically unfavourable reactions to occur (cannot go uphill)
What is meant by “reaction in cells are coupled”?
There are two types of reactions, anabolic and catabolic. The energy in one reaction is used in another, they drive each other. They need carrier molecules to take energy and favour anabolic reactions. The main carrier in our cells is ATP.
What sign is Delta G going to be in order for cells to work?
Delta G has to be (-)
In cells, describe the concept of equilibrium:
- Suppose there is a reaction between Y and X. In this example, the formation of X is energetically favoured in this example. The delta G of Y -> X is negative and the delta G of X -> Y is positive. Because of thermal bombardments, there will always be some X converting to Y and vice versa.
- Suppose we start with an equal number of Y and X molecules, the conversion of Y to X will happen more often than the conversion of X to Y. Because one is energetically favoured over the other.
- Eventually, there will be a large enough excess of X over Y to compensate for the slow rate of X -> Y. This is when equilibrium is attained.
- At equilibrium, the number of Y molecules being converted to X molecules each second is exactly equal to the number of X molecules being converted to Y each second, there is no net ratio.
