Lecture 4 Flashcards
Diffusion is a concept that can be readily explained by the concept of free energy. If a cell is split into compartments such that comp 1 is the initial state and compt 2 is the final state where stuff moves, what would a high concentration of molecules in compartment 2 indicate?
– it would indicate a positive free energy since there is an “Excess” of products. To proceed from state 1 to state 2 would be unfavorable and the movement from state 2 to state 1 would be favorable
– this is because it would be going from low concentration to high concentration
What is oxidation?
process in which chemical substance changes bc of addition of oxygen
– defined as removal of electrons
ex: oxidation of nutrients such as carbohydrates or fats provides cells w/ free energy for synthesis of ATP
Difference between reducing agent and oxidizing agent
Reducing agent –> the one donating/losing electrons or being “reduced” –> one being oxidized
Oxidizing agent –> the one gaining electrons –> one being reduced
T or F, the transfer of electrons to the acceptor may also be accompanied by H+ or H+ can be liberated into solution
True
Redox reaction are a useful chemical reaction that drives important processes in our body, such as the generation of ATP. A complex in the ETC, one of the final steps of glucose metabolism, complex A of the ETC is often called NADH dehydrogenase where the overall process involved the removal of a proton from NADH and the movement of electrons down the chain. Based on this description, is the relationship between complex A and NADH?
A) NADH is the reducing agent while complex A is being oxidized
B) NADH acts as the species that takes electrons from complex A and complex A is the species that donates electrons
C) complex A is acting as the oxidizing agent and NADH is acting as the electron acceptor
D) NADH is the reducing agent whereas complex A is acting as the oxidizing agent
D
What is the relationship between voltage and ability to reduce and oxidize?
higher/positive voltage are better oxidizing agents (accepting electrons) whereas more lower/negative voltage (losing electrons) are better reducing agents (donating electrons)
Oxygen is known as the strong electron acceptor in the final portion of the ETC. This final step in the chain where oxygen essentially steals the electrons from the chain is needed to ensure the ETC is continued and the proton gradient is maintained to allow ATP generation. Based on the information, which description best fits oxygen.
A) It would have a very positive voltage
B) when put into a H+/H2 test cell and used as the reference, electrons would tend to move from the oxygen to the hydrogen cell
C) it would tend to be a very strong reducing agent
D) oxygens ability to electron accept is barely due to its electronegativity
A; because oxygen is stealing electrons from chain –> so then it becomes acceptor
What is the relationship between standard free energy and the electron voltage of a cell in a redox reaction. How do you find the change in voltage?
- free energy at biochemical standard conditions is equal to the negative amount of electrons involved in the reaction, the faraday constant, and the change in voltage.
- -> delta G = -nFdeltaE
– you substract the electron acceptor (A) minus the electron donor (D).
–> delta E = electron acceptor - electron donor
What does a negative vs positive voltage change mean in terms of the hydrogen reference cell which is held at 1M?
– a negative potential means that electrons tend to move from the sample studied to the reference cell
– whereas a positive potential means electrons tend to move from the reference cell to the sample studied cell
You are studying the effects of a reaction in a cell by creating similar conditions in lab. You react cytochrome b (3+) with alpha ketoglutarate to form the products cytochrome b (2+) and succinate. Would this react be favorable or not favorable energetically? The Eo of cytochrome b is +0.07 and the Eo of succinate is -0.67
– Yes. the change in voltage is calculated as Eacceptor - Edonor.
– In this example, since cytochrome b is gaining a electron, it is the acceptor so the other molecule must be a donor.
– 0.07- -(0.67) is a positive value.
– Since free energy = - #electrons F Eo, the free energy will remain negative and therefore be favorable.
What type of bond links nucleic acids? Are they covalent?
– phosphodiester linkages
– yes
DNA and RNA hold several similarities in their structure. They both contain a pentose sugar with phosphates in their ring and a nitrogenous base. One big difference between DNA and RNA is that RNA has a hydroxyl group on its pentose sugar. Why might this indicate why DNA is more likely to be the universal hold of genetic information among eukaryotes?
– the hydroxyl group on the RNA can act as a nucleophile and cleave the phosphodiester bond.
– this will result in cleavage of the covalent bond and essentially degradation of the structure.
– This is unfavorable since the purpose of acting as a storage of genetic information is disrupted as RNA would be able to self cleave.
A structure of ATTAGTAATA is found within the portion of DNA in an organism. This organism has internal regulations that ensure the temperature is constant and favorable for the body to act optimally. Suppose over time the the temperature of the organism had increased as a result of increased metabolic activity that has been favored. Based on your knowledge of temperature and its effect on on DNA, would you expect that mutations to bases that would increase the number of GC to occur and why?
– This could be a favored mutation. Since GC pairs have more hydrogen bondings, they will be more resistant to denaturation by the increased body temp
True or false. The purines are bigger than the pyrimidine bases and it is probably that you would expect them to have a larger contribution to the sterics (spacial arrangement of molecules) of DNA/RNA
true
What is the difference between a nucleoside and a nucleotide?
- nucleoside = base + sugar
- nucleotide = base + sugar + phosphate group (NMP)
