Biochemistry Sheet 30 PDF

30 Tala Alkaiam Saleen Abu Mushref Nafez Abu Tarboush 1  Activation- Transfer Coenzyme 4- PLP: Inactive: Pyridoxine (B6). Active: Pyridoxal phosphate (PLP) The vitamin (B6) is oxidized into aldehyde then a phosphate gr...

30 Tala Alkaiam Saleen Abu Mushref Nafez Abu Tarboush 1  Activation- Transfer Coenzyme 4- PLP: Inactive: Pyridoxine (B6). Active: Pyridoxal phosphate (PLP) The vitamin (B6) is oxidized into aldehyde then a phosphate group is added to form the PLP. Function: Metabolism of amino acids via reversible transamination reactions Transaminases: are enzymes that play a crucial role in amino acid metabolism. They catalyze the transfer of an amino group from an amino acid to a keto acid( forming a new amino acid and a new keto acid).This process is essential for the synthesis and breakdown of amino acids. Mechanism:  Reactive aldehyde forms a covalent bond with the amino groups.  Ring nitrogen withdraws electrons from bound amino acid. Oxidation- Reduction Coenzymes  A large number of coenzymes that don’t form covalent bonds with the substrate, but rather bind to the enzyme.  Most common: a- NAD+ (B3,Niacin) b- FAD (B2,Riboflavin)  Others: work with metals to transfer single electrons to O2 (Vitamins E & C).  Dependence on the enzyme for additional specificity of substrate & additional catalytic power. 2  A- NAD+: (Nicotinamide Adenine Dinucleotide)  It forms from the modification of Niacin (B3), and its functional group (C opposite to N) accepts a hydride ion (H-) from the substrate. (This involves the acceptance of two electrons at once, meaning there will never be a form of NAD+ that only has one electron)  The substrate has two hydrogen atoms. Once it binds to the enzyme, the two hydrogens dissociate forming H- that binds to NAD+ and H+ that dissolves into the solution, and a keto group (C=O) is formed.  (ADP) portion of the molecule binds tightly.  NAD+ and NADP+: are both modifications of niacin. They share the same function yet they differ in the substance that binds to the ribose of the Adenine. If this substance is a hydrogen atom, then NAD+ is formed, but if it is a phosphate group then NADP+ is formed. This difference is due to organizational purposes only.  NAD+ is usually involved in catabolism reactions (e.g. glycolysis, the Citric acid cycle) while NADP+ is involved in anabolism reactions (e.g., the Calvin cycle, fatty acid synthesis. (The examples mentioned here are used to further aid the understanding. They aren’t meant to be memorized) 3   The role of the enzyme’s Histidine is to interact with the hydroxyl group (-OH) of lactate, weakening the bond between the oxygen and the hydrogen atom. This interaction facilitates the transfer of the hydrogen atom, making it easier for NAD+ to accept the hydride ion (H-) from lactate. B- FAD : (Flavin Adenine Dinucleotide)  It forms from the modification of Riboflavin (B2).  Flavoproteins: are conjugated proteins that contain Flavin derivatives (FAD and FMN) and are involved in oxidation-reduction reactions.  Both FAD and FMN (Flavin Mononucleotide) serve as prosthetic groups, meaning they are tightly bound to the enzyme.  Both FAD and FMN accept two electrons, but due to functional specialization, some reactions use FAD while others use FMN.  FAD has the ability to transfer 2 electrons, similar to NAD+, but does so in a sequential manner. While NAD+ accepts electrons as a hydride ion (H-) in a single step, FAD accepts electrons one at a time. (There is a gap in the acceptance of the first and second electron). In the first step, FAD accepts one electron, forming a radical. In the second step, FAD accepts the second electron, becoming fully reduced to FADH2. The intermediate radical form makes 4  FAD unstable and pretty harmful in its one electron state, so it’s never found free in a solution. Instead its always bound to enzymes, where it functions as a prosthetic group to stabilize its radical form and facilitate electron transfer. In contrast, NAD+ doesn’t form a radical intermediate, as it always accepts a pair of electrons in the form of hydride ion (as mentioned earlier). Consequently, while NAD+ has defined properties for electron transfer, FAD’s behavior depends on the surrounding enzymes, which influence its redox activity.  Reactions that involve FAD: 1. Succinate dehydrogenase 2. Pyruvate dehydrogenase complex 5  Catalytic Metals  Metals can be tightly bound (metalloenzymes) -removal of the metal causes denaturation of the enzyme- or loosely bound (metal-activated enzymes).  They act as electrophiles (attract electrons).  Metal-activated enzymes; the metal either required or enhances activity (Mg2+, Mn2+, Ca2+, K+).  Phosphofructokinase & TPP;(Mg2+) is required to coordinate the phosphate groups on the ATP for a successful reaction (chelation). Fructose-6-phosphate + ATP → fructose-1,6-bisphosphate + ADP 6 Alcohol dehydrogenase (ADH):  Removes hydrogen from alcohol, as its name implies, catalyzing the oxidation of alcohol to an aldehyde.  Histidine pulls electrons from serine which in turn pulls electrons from the alcohol, oxidizing it into an aldehyde. The electrons are then transferred to NAD+ in the form of hydride ion (H-). Throughout this process, Zinc stabilizes the oxyanion produced when the proton dissociates from the hydroxyl group (-OH), ensuring the reaction proceeds efficiently. Although Zinc doesn’t directly participate in the redox reaction, it plays crucial role by facilitating the reaction through charge stabilization.  Zinc in ADH is as Histidine in lactate dehydrogenase, where histidine helps facilitate the reaction but doesn’t directly participate in the electron transfer. 7  Kinetics  Chemical reactions can be described using two theories: 1. Thermodynamic theory which measures only the energy differences between reactants and products to determine if a reaction is favorable, without considering the steps in between. 2. Kinetic theory, which focuses on the reactions pathway, including the steps and energy barriers, to determine the reaction rate.  Biochemical Kinetics: the science that studies rates of chemical reactions which means studying the pathway between the reactants and products. 8  An example is the reaction (A P), The velocity, v, or rate, of the reaction A P is the amount of P(product) formed or the amount of A (reactant) consumed per unit time, t. That is The order of the reaction and the rate constant  A multistep reaction can go no faster than the slowest step v = k(A)n1(B)n2(C)n3  (n1+n2+n3) is the overall order of the reaction  The rate constant (k) in a chemical reaction is a measure of how quickly the reaction proceeds. It is influenced by the activation energy (Ea), which is the minimum energy required for the reactants to transform into products. the higher the activation energy (energy barrier),the smaller the value of k. 9 Zero order: The reaction rate is independent of the contraction of any reactant. In this case, the rate is constant. (rate=k) First order: The reaction rate is directly proportional to the concentration of one reactant. (rate=k[s]) Enzyme kinetics  Enzymes can follow both orders (zero & first). The reaction velocity increases with substrate concentration until it reaches the Maximal Velocity, at which all the active sites on the enzyme are occupied by substrate molecules, and the enzyme becomes saturated.  The limiting factor in this process is the availability of active sites. Initially when substrate concentration is low, there are plenty of available active sites, so the reaction follows first-order kinetics, where the velocity increases as more substrate binds to the enzyme. However, as substrate concentration continues to increase, the reaction rate reaches a plateau (zero-order kinetics), meaning all the active sites are occupied, and further increases in substrate concentration do not increase the reaction rate. At this point, the reaction rate becomes stable and has reached its maximum velocity.  Enzymatic reactions can exhibit simple behavior or complex behavior (such as allosteric regulation).  Simple enzyme behavior: As the concentration of the substrate rises, the velocity increases until it reaches a limit (Vmax). This behavior is typically described by Michealis-Menten kinetics.  Enzyme-catalyzed reactions often display hyperbolic (saturation) plots, where the rates increase steeply at low substrate concentrations and levels off at high concentrations.  The maximal reaction rate (Vmax), is reached when all the enzyme’s active sites are fully occupied by substrates, and adding more substrate will no longer increase the reaction rate. At Vmax the reaction 10  exhibits zero-order kinetics, where the rate becomes independent of the substrate concentration because the enzyme is operating at its maximum capacity.  Vmax reflects the enzyme’s turnover number, which is the number of substrate molecules converted into product per unit of time by a single enzyme molecule when its fully saturated with substrate. ‫تمت كتابة هذا الشيت عن روح والدة زميلنا عمرو رائد من دفعة تيجان‬ ‫دعواتكم لها بالرحمة والمغفرة‬ Thank you 11