BIOL 541 1st Edition Lecture 10 Outline of Last Lecture I. Allosterism Outline of Current Lecture II.Co-enzymesIII. Co-factorsIV. General MechanismCurrent LectureBiochem Lecture 10: Co-enzymesCobalamin: Vitamin B12. It is one of the lsrgest with center of Cobalt anf not Fe as in heme. Side chains are adenine nucleotide with sugar residue as side chains. It is not well absorbed from the gut but requires intrinsic factor such as protein secreted by the cells of the stomach. Pernicious anemia develops if the system is affected. Treatment is given by B12 injections administered by medical staff.Reaction Catalysis: Reduction reaction of nucleotide such as oxygenated nucleotide to deoxygenated nucleotide forsynthesis of DNA: Catalysis transfer reaction occurs where the x group is flipped to adjacent carbon by pulling off the H and free radical H is formed. The X group hops into the space and H is added to the adjacent C. X can also be –OH group.1.Diol dehydratase: OH +H forms water which is removed as flipping causes both –OH groups close together. Thus, the final product is from a diol to aldehyde.These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.2. Ethanolamine Ammonia lyase: H switches with H2N and H2N and H form ammonia. The end product is aldehyde.3. C-C bonds are strong but can be switched. Glutamat mutase can flip COOH to another C forming gamma- acid.Co- factors: In- organic molecules example, metal ions which help enzymes.1. Act as electrophilic groups: They are very positively charged and pull electrons as extreme liking for electrons. This creates a strain on the bonds created so they become susceptible to attack. It can be used to co-ordinate electronegative groups, for example:a. Zn in carboxy peptidase A.b. Mg phosphorylase where Mg regulates the ezyme that removes the phosphate group and adds Mg instead.c. Mn arginase in urea cycle.2. Valence change involved in oxidation/ reduction reaction:a. Fe occurs either as ferric or ferrous forms or in heme as peroxidase or catalyse.Non heme as Fe is held in place by sulphur of cysteine.Example, nitrogenase in plant root nodules have bacteria that fix nitrogen by converting them to ammonia.b. Cu- occurs as cuprous or cupric in cytochrome oxidase in the electron relay system.c. Se- in selino cysteine which is a co-factor glutithymine peroxidase.d. Mo in Zantin oxidase.e. Ni detoxifies CO to carbon dioxide in organisms.General types of Mechanisms:1. Approximation- Enzymes bring reactants together by increasing concentration and increasing speed of reaction.2. Destabilization- The catalytic site can not fit substrate perfectly but in transient state, substrate distorted and susceptible to further reaction.3. Acid base catalysis involves residues in enzymes that donate or take H. Examples are Glutamic acid, Asparatic acid, HIS, LYS, TYR, and CYS. These enzymes can be protonated to act as acid or deprotonated to act as base. Ionization depends on pK3 as effected by local environment. Example lyzozyme is an enzyme that is regulated by pH.4. Covalent Catalysis: The intermediate actually forms covalent (temporary bond with enzyme).SER –OH -------- ESTER with various fatty acids or carboxylic acid.CYS- SH ------Thiol esterLYS ----- shifts bases with aldehyde.HIS ----- Phosphate transfer group imizidiol transiently phosphorylated.Enzyme regulation:1. Enzyme regulation occurs in levels for 2 types of enzymes:a. Constitutive are those enzymes that form core metabolic cycles. Enzymes are always needed and made. Even constitutive enzymes have variations as separate genes or alternate splicing to form isozymes differ in terms of location and regulation.b. Induced are the enzymes of specialized pathways and waste of energy if not needed. Example: Cortisol is elevated during fasting as there is increase in gluconeogenesis where amino acids are converted to carbohydrates. If carbohydrates are already present, then those enzymes are not needed.2. Temperature and pH:Increase in temperature causes an increase in energy in molecules, thereby increasing random movement and increasing the chance of collision. Therefore, increasing temperature increases reaction rate. Increase in temperature is only favored for a certain point. Protein starts becoming denatured at 40- 45 degrees celcius.Increasing pK3 needs to be optimal and related to groups needed to be ionized. As homeostasis mechanism, constant pH and temperature is maintained. In reality pH fluctuates within cells as growth factors are elevatedbetween 0.1 to 0.3. This increase is huge in Log scale. pH increase intergeres as acid is used in catalytic mechanism. Cell destruction of cell by stimulating enzymes involved with signaling and electron transport system. Therefore, increase in pH increases growth factors as enzymes needed for growth are increased. Stimulating proton pumps so growth occurs.Hibernation in mammals in winter, their temperature decreases for ambient reasons and 1-2 degrees fluctuation is seen between morning and evening. Temperature change also occurs during metabolism changes. These are secondary temperature changes.Primary temperature changes occurs during fever where the increase in temperature favors WBC mobility for phagocytosis and reduces endotoxins secreted by bacteria.3. Allosterism: Ability of small molecule to bind to enzyme and alter its affinity. If active site is bound- competitive inhibitionIf other site is bound – non- competitive inhibition.Catabolic enzymes need energy calculations.a. Energy: If energy is needed then ATP/ADP is considered where enzymes have allosteric sites for energy levels.ATP- high energy- inhibitoryADP-low energy- stimulatoryc. NADH/NAD (electron transport system): H + oxygen to form water. NADH forms ATP in electron transport chain, therefore inhibitory. NAD is stimulatory in nature.d. Negative feedback: Product builds up and promoted feedback inhibition. In competitive inhibition, both substrate and product compete and product outcompetes the substrate.e. Forward reactions are substrate induced as presence of substrate speeds up reaction due to allosteric sites.f. Second messengers- small molecules used by hormones for carrying. Activation of protein kinase A (PKA) by cAMP (allosteric dependent kinase).4. Covalent