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 Sheet 2, Dr.Nafeth, by Dima Affaneh 7\2\2012

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Majed Sharayha

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PostSubject: Sheet 2, Dr.Nafeth, by Dima Affaneh 722012   Fri Feb 10, 2012 6:54 am

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((( بسم الله الرحمن الرحيم )))
Last time we talked about the bioenergetics of the cell, and how can we make energy from the cell…
- As we know pyruvate is a product of glucose, Fatty acids + amino acids can also be oxidized and everything is converged in the end to make acetyl co-enzyme (A) that enters the crips cycle "the TCA cycle" giving out CO2…

- NADH and FADH2 both of them enters the oxidative phosphorylation which is the electron transport chain to make ATP at the end…

- In the oxidation-reduction reaction "transport of electrons" :
electron transport from the fuel which is the food supplement that we take by oxidation to NAD+ & FAD forming NADH & FADH2 which are filled with electrons that enters the oxidative phosphorylation giving the electrons to the oxygen creating the proton electro chemical gradient across the membrane and in the end to make ATP …
- Oxidation-Reduction reaction is also called redox reaction which is the reaction that includes the transport of electrons "since there's breaking and formation of bonds" and in any oxidation reduction reaction we have pair of chemicals "electron donor and electron acceptor"
in humans >>> the electron donor is the food which is the fuel
the electron acceptor is the NAD+ FAD NADP

-What is the difference between the NAD+ and FAD???
they differ in their mechanism…
NAD+ >>> have less electrons and that is obvious since its positively charged + it receives the hydrogen as hydroid ion which means that it takes the hydrogen as "H-" forming NADH … and since the hydrogen ion usually is not found alone but as an atom "H2" so it takes one of them "H-" and leave the other one devoid of electrons so it goes to the solution as "H+" proton…
FAD >>> takes two hydrogen ions from two different atoms "two hydrogen atoms (different sources) " to take 2 electrons "it's not a must to take them at the same time" forming FADH2 (filled with electrons) that gives electrons to the final electron acceptor in the electron transport chain which is the oxygen…
-We should know that the best electron acceptor is the O2 …

-Reduction potential >>> is a measure in volts of the energy change when the compound accept electrons…
so the more (+) the reduction potential is the more hungry it is to get electrons
and the more (-) the reduction reaction is the more electrons available to give "the greater the energy available for the generation of ATP "
and since the oxygen have the highest reduction potential it’s considered as the best electron acceptor…"so it depends on the electronic state"

Note >>> The doctor also said enu the reduction potential is me9fat tafa3ol lal reduction half "nsf aksadeh" and oxidation half "nsf e5tezal" and both of them are equal in energy and electrons…

-Reduction half >>> how much energy we need or how much energy we spend to reduce the compound…

-according to the table found in the slides :
Riboflavin + 2(H+) + 2(e-) >>> Riboflavin-H2 -0.200
(NAD+) + 2(H+) + 2(e-) >>> NADH + (H-) -0.320

- Riboflavin is Ribose + FADH
-those #'s are the voltage "the same as the ones found n any electronic machine" and those #'z are for the reduction half only…
- for NAD+ to become NADH we're transferring ( – 0.320 mv ) so that means here we have excess in NADH
- FAD (-200 mv) but in real it's (-0.18mv) but because it's with ribose it became (-0.200 mv)
so NADH can give more energy than FAD and that depends on the reaction that we are doing…

-Now what is the relation between ΔG and ΔE ?
ΔG is the voltage difference and ΔE is the energy difference
and according to following equation (ΔG= -nf ΔE) when we increase ΔE , ΔG increases too…and you can easily calculate ΔG if you know ΔE using this equation since both of n + f are constants… "n= # of electrons f= faraday constant"

- the more (-) the reduction potential or the more (-) is the difference between potentials >>> the higher the difference in energy " ΔE "…

-NAD+ vs. NADP >>>
the difference between them is a phosphate group "which is a space", the NADP contain an extra phosphate so the space in it is larger so its larger in size … and since its large in size we rarely find enzymes that can work n it…
In all the reactions we break and form bonds by oxidation forming NADH or NADP and there's enzymes that take NAD+ or NADP and those enzymes works according to the lock and key law so if we have a phosphate it'll disrupt so it can’t take them anymore so there is enzymes which are specialized to transport NAD+ and others for NADP and RARELY you find enzymes that can deal with both of them together…

-In the fatty acid synthesis and the decalcification reaction that happen inside the lysosomes or perisosomes , NADP is the co-factor in it not the NAD…

-the pentose phosphate pathway >>> is a pathway found in the cells to form Riboses "the five sugars" that are used in DNA so when we synthesis it using glucose 6 phosphate dehydrogenase "which is an enzyme" that uses NADP not NAD…

-Sooo enzymes that use NADP are >>>
1-Glucose-6-phosphate dehydrogenase enzyme
2-pentose phosphate pathway
by moving the electrons using NADP that works as electron receiver becoming NADPH that gives electrons to continue the pathway…

-Palmitate "a fatty acid" vs. Glucose…Which one of them have more energy than the other???
Palmitate because >>>
1- it contain more bonds so a higher electronic value…
2-glucose is a ring structure so it's more stable than palmitate "less electrons"

- more bonds >>> more energy >>> more synthesis of ATP

-Cellulose is found in wood so when we burn it we break the bonds in it forming energy in the form of heat and the oxygen oxidize and turn into CO2 … but in humans we can't use it why?
because we don't have enzymes that have the capability of breaking these bonds or transferring the electrons to NADP NAD or FAD… so that means we can't use everything and process it to get energy from it… just like cholesterol …

-90% of the O2 that we breath enters the electron transport chain forming ATP through the oxidative phosphorylation…
-But can we make ATP without the use of O2??
yea for ex. In the >>> 1- muscles "forming lactate"
2- kidney medulla "which is designed to make anaerobic glycolysis more than oxidative phosphorylation"
-kidney medulla is a nephron "the basic structural and functional unit of the kidney", when water enter the nephron it sends the electrons out and in then it enters the cycle n kidney medulla so then it can reabsorb the nutrients "sodium + electrolytes + potassium"
-process of anaerobic glycolysis >>>
glucose + high energy bond + phosphate intermediate
turns into pyruvate and NADH "which means energy" but we can't use the NADH because it's used in the conversion of pyruvate into lactate…
- the rest of the O2 we breath "10%" some enzymes use it not for the purpose of ATP , called enzymes of oxidases + oxygenases that use it as a substrate…

-What is the difference between oxidases and oxygenases???
oxidases >>> enzymes that mainly transfer the (electrons) to the substrate…
oxygenases >>> enzymes that transfer the oxygen to the substrate … and its divided into monooxygenase "add 1 oxygen" and dioxygenase "add 2 oxygens"

-Sulfar + 1oxygen >>> Monooxygenase
Sulfar + 2oxygens >>> Dioxygenase
Sulfar + 1oxygen as hydroxyl group >>> hydroxylases
- as we said before oxygen is the best electron acceptor so when the electrons goes to the oxygen it should be a fast process cuz oxygen is the most hungry to get electrons but this doesn't happen due to the electronic state around the oxygen >>>
electrons around the oxygen are found in pairs so it doesn’t allow the electrons from coming closer "since all of them try to become more stable" so it can't take electrons quickly and this what makes this process slow "process of transferring electrons of oxygen become slow" so to increase the speed of this process the enzymes in the cells are designed to have metals in it "that can stabiles the high oxidation state" like the iron that binds the oxygen to create a bond that decrease the electronic state around the oxygen so the bond become easier and the transfer of electrons become easier also…for ex. hemoglobin contain heme that contain iron and the oxygen binds to the iron since its easier for it to bind there...

- oxidase higher the oxidation state which add 2 oxygens "Dioxygenase"
-energy balance >>> 70% of the energy that we are taking goes to the basal metabolic rate to the major functions of the major organs in the body which are the heart kidney liver exercising muscles ...etc
- the efficiency of the ATP machinery is not 100% effective because some of it is lost in the form of heat so its efficiency is almost 70% but what are the conditions that lower this efficiency??? "at the molecular level"
all the oxidation phosphorylation reactions "formation of ATP" happens while pumping of electrons outside of the membrane to create an electro chemical gradient "more + out = more hydrogen out" but the leakage of some of these protons back to the inside of the matrix decreases the efficiency of the ATP machinery…
"Increase and decrease in the electrochemical gradient changes the PH and the electricity which causes the leakage of protons back inside and that’s what causes the decrease in the efficiency of ATP"

Q1 : The highest energy phosphate bond in ATP is located between which of the following groups?
(A) Adenosine and phosphate
(B) Ribose and phosphate
(C) Ribose and adenine
(D) Two hydroxyl groups in the ribose ring
(E) Two phosphate groups
Answer>>> (E) between the two phosphate groups and the bond there is called phosphoanhydride bond "the bond between the 1st two phosphates is 7.3 kcal and if we break the next phosphate bond we'll have also 7.3 kcal but if we break the 3rd bond we'll have 3.4 kcal because the bond is not phosphoanhydride bond "between two phosphate groups" it's between phosphate and carbon…

Q2 : A patient, Mr. Perkins, has just suffered a heart attack. As a consequence, his heart would display which of the following
(A) An increased intracellular O2 concentration
(B) An increased intracellular ATP concentration
(C) An increased intracellular H+ concentration
(D) A decreased intracellular Ca2+ concentration
(E) A decreased intracellular Na+ concentration
Answer >>> (C) increased intracellular "H+" conc. Because the O2 conc. intracellularly Decreases so ATP conc. Also decreases and since there's not enough ATP to pump the sodium out and the protons in, the sodium that is left out go back inside and the protons go out and since we now don't have enough sodium outside to go in the counter transport so sodium is not getting in the cell and protons are not getting out so the proton conc. Inside the cell increases and also sodium conc. Increases inside and Ca2+ also increases because its actively pumped out and since there is no ATP it'll stay inside "to be honest I have no idea what did I just wrote I didn't understand it but that's exactly what the dr said"

Q3 : Which of the following bioenergetic terms or phrases is correctly defined?
(A) The first law of thermodynamics states that the universe tends towards a state of increased order.
(B) The second law of thermodynamics states that the total energy of a system remains constant.
(C) The change in enthalpy of a reaction is a measure of the total amount of heat that can be released from changes in the chemical bonds.
(D) Δ G⁰* of a reaction is the standard free energy change measured at 37C and a pH of 7.4.
(E) A high-energy bond is a bond that releases more than 3 kcal/mole of heat when it is hydrolyzed.
Answer >>> (C) is the right answer "enthalpy is the difference in the heat of a system and according to this equation (ΔG=-nfΔE) this is right answer" …
(A) is wrong because the first law states that the total energy of a system remains constant. And (B) is wrong because the 2nd law states that the universe tends towards a state of increased order … (D) is wrong because the standard conditions are room temperature "almost 24-25" and PH 7…and (E) is wrong because the high energy bonds releases 7 or more kcal/mole…

Q4 : Which statement best describes the direction a chemical reaction will follow?
(A) A reaction with a positive free energy will proceed in the forward direction if the substrate concentration is raised high
(B) Under standard conditions, a reaction will proceed in the forward direction if the free energy _G__ is positive.
(C) The direction of a reaction is independent of the initial substrate and product concentrations because the direction is
determined by the change in free energy.
(D) The concentration of all of the substrates must be higher than all of the products to proceed in the forward direction.
(E) The enzyme for the reaction must be working at better than 50% of its maximum efficiency for the reaction to proceed
in the forward direction.
Answer >>> (D) is the right answer… (A) is wrong because it should be negative … (B) is wrong because it should be also negative … (C) is wrong because it depends on them…(E) is wrong because if there is enzyme or no the reaction will proceed forward but the enzyme only help to make the reaction faster…

Q5 : Which of the following statements correctly describes reduction of one of the electron carriers, NAD+ or FAD?
(A) NAD+ accepts two electrons as hydrogen atoms to form NADH2.
(B) NAD+ accepts two electrons that are each donated from a separate atom of the substrate.
(C) NAD+ accepts two electrons as a hydride ion to form NADH.
(D) FAD releases a proton as it accepts two electrons.
(E) FAD must accept two electrons at a time.
Answer >>> (C) is the right answer…(A) is wrong because it accepts only one… (B) is wrong because it accepts a hydride ion…(D) is wrong because NAD+ is the one that takes H- from a hydrogen atom leaving a proton behind that go to the solution as H+… (E) is wrong because its not a must to be at the same time…

Introduction for the next lecture :

-The process that makes ATP inside the cell >>>
it’s a sequence of enzymes "oxidation-reduction reactions" few oxidation give you electrons that goes to the NAD NADP or FAD to form NADH FADH2 that gives electrons to the enzymes that are found in the electron transport chain and continue to a sequence of ATP synthesis where it can make ATP…

-what are the requirements for ATP to take place?
1- electron donor "NADH FADH2" –contain electrons-
2-electron acceptor "O2 which is the best"
3- intact mitochondrial membrane , Why???
because of the electronic gradient cuz when the electrons move the protons starts to pump out but some of the protons leak in again so that will decrease the efficiency of the reaction so in the electron transport chain the enzymes must be intact "have no genetic problem so it won't make shortage in any of them …

-How the electron transfer happens???
Fuel oxidation that gather to form co-enzyme (A) and enter the crips cycle forming at the end NADH or NADH2 "filled with electrons" which give electrons to NADH dehydrogenase…
-NADH remove the H >>> we are dehydrogenating it "the substrate" so the product will be NAD+ cause we are taking H- out of it which is filled with electrons that if enter to complex 1 which is NADH dehydrogenase it will have 2 electrons in term it'll give it's 2 electrons to something called co-enzyme (Q) which is known as quenoids "chemical compound that forms a cyclic compound with 2 oxygens in a high oxidation state where it can accept electrons . and the co-enzyme Q receive electrons from H- which send it from complex 1 to complex 3 and return as co-enzyme Q…

complex 2 >>> succinate dehydrogenase also through FAD receives electrons and give them to complex 3…

-however we have more than a complex inside the cell that can give electrons so the sequence become :
complex 1 >>> complex 3
complex 2 >>> complex 3
other compounds >>> complex 3
so there's no direct communication between complex 1 and complex 2…

complex 3 >>> cytochrome BC 1 complex "cytochrome means its an enzyme with heme inside it - heme type B and C -" complex 3 receives the electrons from co-enzyme Q and then give it to cytochrome C oxidase "which is complex 4" that is found in the intra membranous space…then O2 will be reduced converting it to water…

the electrons while transferring from complex 1 to complex 3 then to complex 4 pumping of protons occur so the electrons are losing energy because of the pumping of protons…
electrons loose 16 kcal from complex 1 to 3 and another 16 kcal from complex 3 to 4… and that’s how the electro chemical gradient happen…

Done By : Dima Affaneh
Biochemistry sheet #2
Dr Nafeth…
Best Wishes
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