Energy and Catalysis Flashcards
(25 cards)
How would you define “metabolism” in cells?
= the sum of all the chemical reactions it needs to carry out to survive, grow, and reproduce
What are the 2 opposing streams of chemical reactions?
1) Catabolism = breaking down foodstuffs into smaller molecules and thereby generating useful energy
2) Anabolism = utilizing the energy to synthesize more complex molecules
What does the second law of thermodynamics postulate?
= that in any universe or isolated system, the degree of entropy increases
= system will change spontaneously toward those arrangements that have the greatest probability/entropy
- measure of the system’s disorder = entropy
However, living cells generate order - how come they don’t violate the second law of thermodynamic?
Cell is NOT an isolated system - it receives energy from the environment (e.g. foodstuffs, light) -> uses the energy to generate an order within itself -> some energy is lost/exposed of in the form of heat (entropy) -> heat dispersed into the surroundings (this heat is than used in the machinery to create order again)
What is the first law of thermodynamics? How does a cell conform to it?
= the fact that energy cannot be creater nor destroyed but only converted from one form to another
- E.g. cells convert sunlight energy into chemical bonds of sugars during photosynthesis, when cell breaks down the foodstuff molecules get converted into heat energy
How does (in general) photosynthesis work?
- first stage: sunlight energy captured and temporarily stored as chemical bond energy in specialized molecules = activated carriers
- molecules of water split -> which produces O2
- second stage: activated carriers are used to drive a carbonfixation process -> sugars get manifactured from CO2 (could also generate amino acids, nucleotides, fatty acids)
What other large process do cells perform to obtain energy?
Cell respiration (complimentary to phosynthesis)
- In the presence of oxygen the most energetical stable forms of C is CO2 and of H is HO2
- cell can derive energy from sugars by allowing molecules to bind in this preferred way => C and H become oxidated
What exactly is oxydation? What is the opposite?
- Oxidation = chemical reaction in which one atom looses electrons (more positive)
- E.g. when Fe2+ is oxydazed in becomes Fe3+
- Reduction = chemical reaction in which an electron gets added to an atom (more negative)
- e.g. when Cl receives an electrone it becomes Cl-
-> the two processes always happen simultaneously
NOTE: applies also in polar covalent bonds e.g. CO2 - C is oxidized while O reduced
What makes it tricky to think about oxidation/reduction in C-H bonds? How can we easily overcome that?
Usually when I molecule pics up an electron it also gets H+
-> even though protons are alsi involved = hydrogenation, the addition is still a reduction
-> dehydrogenation = reactions that get rid of H+ alongside e- -> still oxydation
Solution: count C-H bonds
- If C-H bond got added = reduction
- if C-H number decreased = oxidation
How would you define “free energy”? What in general should be remembered about chemical reactions?
Free energy = energy that can be harnessed to work as a drive for chemical reactions
- release of it reflects the “loss of orderliness”
- also refered to as G
- Chemical reactions proceed in the direction that leads to a loss of free energy (they go “downhill”) -> more energetically favourable
- since chemical reasctions are about changing one molecular state into another we look at free-energy change, or Delta G
What do we mean by “activation energy”? How does it relate to the fact that paper doesn’t just burst into flames?
Sometimes molecules do NOT reside in their most energetically favorable/stable forms
- e.g. not all carbon and hydrogen immediatelly turn into CO2 and H2O (otherwise we would evaporate and paper would spontaneously burn)
-> this is because they achieved a different stable state and there is an energetic barrier that needs to be exceeded to achieve the most favourable energetical state (i.e. energy has to be added) = this additional energy we call the activation energy
- e.g. for paper it’s the flame we light up -> for cells the “pushers” come in a form of enzymes
How exactly do enzymes do that? How can we in general terms call these substances? What could be an advantage of enzyme over temperature change?
Enzymes bind to one or more molecules (=substrates) and hold them in a way which alters binding sites -> reduces needed activation energy -> facilitates certain chemical reactions
In general substances that increase rate of chemical reactions in this way = catalysts
Advantages:
- quicker, easier to attain (+more controlled)
- enzymes are highly selective
- enzymes don’t change after their use -> could be utilized repeatedly
Are all proteins enzymes? And are all enzymes proteins?
No! Only proteins that catalyse a reaction are called enzymes. Many proteins do not catalyse reactions and are thus not enzymes. This does not mean that non-enzyme proteins are not useful.
For instance, microtubilin are non-enzymatic proteins that are vital for cells to function.
Finally, not all enzymes are proteins. Some reactions are catalysed by other molecules, often RNA. Such enzymes are also called ribozymes (from ribonucleotide enzymes). The catalytic activity of a ribosome comes for example from an RNA-molecule.
What is the connection between Delta G and chemical reactions? Give examples
If Delta G = amount released of disorder when a reaction takes place
-> Energetically FAVOURABEL are those that create disorder by decreasing free energy on the system = they have NEGATIVE Delta G
- reactions can occur spontaneously only if Delta G is negative e.g. NaCl dissolving in water
- BUT reactions could still be slow
-> Energetically UNFAVOURABLE, create order in the universe = they have a POSITIVE Delata G
- e.g. creation of peptide bonds between amino acids -> can NOT occur spontaneously -> has to be coupled to a second reaction with negative DG large enough so that the net DG is also negative
NOTE: enzymes are able to couple favourable and unfavourable reactions to create a biological order
So what 2 things does the continuing of a reaction depend on?
- The energy stored in each individual molecule
- Concentration of the molecule in the solution
- If I have Y->X reaction -> the concentration of product X will increase while the concentration of substrate Y will decrease
=> as the ratio shrinks Delta G will become less negative => reaction eventually cannot run anymore
- If I have Y->X reaction -> the concentration of product X will increase while the concentration of substrate Y will decrease
What is meant by chemical equilibrium and why do we not observe it in cell?
= state at which the concentrations of substrates and products are evened out that every chemical reaction is trying to achieve -> Delta G = 0 -> no reactions forward or backward
- In cells impossible to achieve:
- they need to keep on exchanging information
- usually product of one reaction used as a substrate of a subsequent -> the accumalation doesn’t exceed as much
Considering Delta G depends on concentration how do we predict whether a reaction has Delta G negative enough to drive energetically unfavourable reactions?
To compare the reactions we can use the Standard free-energy change, Delta G°
- it is independent of concentration and only considers the properties of the molecules based on their behavior in ideal conditions (i.e. where concentration of all molecules is 1 mole/liter)
- The equation:
- RT = gas constant = 0.616
- If concentrations are the same -> we get rid of the right side (ln 1 = 0) => then the Delta Gs are equal
NOTE: By knowing the equilibrium constant (K) one can predict which way will reaction preceed and how far it will go.
NOTE: How would we calculate the equilibrium constant K for two reactants leading to a single product (since that happens in cells more often than X->Y)?
The principle is the same, concentrations are just combined
- the multiplication is there due to a collision od the molecules
NOTE: free energy plays a role in non-covalents bonds as well (e.g. linking proteins together)
Two molecules will bind only if the free-energy for their interaction is negative (free energy resulting from the complex product is lower than the sum of the free energies of the individual substrates)
- since equilibrium constant is related to Delta G -> it could be also used to estimate the binding strength of non-covalent interactions
- larger K => greater drop in free energy => tighter bonds
We have 2 sequential reactions X->Y and Y->Z where the former has DG° = +5 kcal/mole and latter has DG° = -13 kcal/mole - how can we make them happen?
The reaction X->Y is unfavourable while the reaction Y->Z is favourable -> in such case we would need to utilize enzyme catalyzing the first suplemmented by enzyme catalyzing the second => DG° coupled reaction in this case yields -8 kcal/mole and becomes thus favourable
One enzyme can capture and process thousands of substrate molecules every second -> how come it can find these molecules so swiftly across cytosol?
Molecules move constantly and rapidly across space thanks to heat energy = diffusion -> they can encounter huge number of molecules on these “random walks”
- small molecules can diffuse over cytosol just as easily as through water
- while enzymes (bigger proteins) will move much slower => encounters with molecules depend on the concentration of substrates (and even at low concentrations a lot of molecules still bump into enzymes)
What happens when enzyme and a substrate meet? What holds them together or separates them?
=> formation of enzyme-substrate complex
- stabilized by multiple weak bonds (hydrogen bonds, van der Waals attractions, electrostatic attractions) -> form a product
- product persists until random thermal motion dissociates them again (thus if substrate doesn’t fully match the enzyme -> tbonds too weak -> immediate dissociation)
-> enzyme is free to bind again
How does the relationship between enzymes and substrates looks like? (as if we had a fixed concentration of an enzyme and increasing concentration of a substrate)
- As we increase the concentration of the substrate the graph approxiamates a linear trend -> more on more binding sites occupied -> rate tapers off -> achieves maximum = Vmax
